/***************************************************************************** # Copyright (C) 1994-2008 by David Gordon. # All rights reserved. # # This software is part of a beta-test version of the Consed/Autofinish # package. It should not be redistributed or # used for any commercial purpose, including commercially funded # sequencing, without written permission from the author and the # University of Washington. # # This software is provided ``AS IS'' and any express or implied # warranties, including, but not limited to, the implied warranties of # merchantability and fitness for a particular purpose, are disclaimed. # In no event shall the authors or the University of Washington be # liable for any direct, indirect, incidental, special, exemplary, or # consequential damages (including, but not limited to, procurement of # substitute goods or services; loss of use, data, or profits; or # business interruption) however caused and on any theory of liability, # whether in contract, strict liability, or tort (including negligence # or otherwise) arising in any way out of the use of this software, even # if advised of the possibility of such damage. # # Building Consed from source is error prone and not simple which is # why I provide executables. Due to time limitations I cannot # provide any assistance in building Consed. Even if you do not # modify the source, you may introduce errors due to using a # different version of the compiler, a different version of motif, # different versions of other libraries than I used, etc. For this # reason, if you discover Consed bugs, I can only offer help with # those bugs if you first reproduce those bugs with an executable # provided by me--not an executable you have built. # # Modifying Consed is also difficult. Although Consed is modular, # some modules are used by many other modules. Thus making a change # in one place can have unforeseen effects on many other features. # It may takes months for you to notice these other side-effects # which may not seen connected at all. It is not feasable for me to # provide help with modifying Consed sources because of the # potentially huge amount of time involved. # #*****************************************************************************/ "\n", "! In the following, I have annotated the parameters with the following\n", "! symbols:\n", "!\n", "! (YES) freely customize to your own site\n", "! (OK) don't change unless you have a specific need and know what you\n", "! are doing\n", "! (NO) don't change this!\n", "! (GREEN LAB) Resources here are just those for Green Lab research and have\n", "! no effect on any Consed/Autofinish/AutoReport functions\n", "\n", "!\n", "!\n", "! parameters in the (YES) category:\n", "!\n", "\n", "\n", "consed.printPS: true\n", "! print memory \n", "! (YES)\n", "\n", "\n", "\n", "consed.defaultTagType: polymorphism\n", "! when swiping the consensus in the Aligned Reads Window to create a\n", "! tag, what is the default tag type to be added?\n", "! (YES)\n", "\n", "consed.defaultTagOnConsensusNotReads: true\n", "! when swiping the consensus in the Aligned Reads Window to create a\n", "! tag, by default will the consensus be tagged or the reads be tagged?\n", "! (YES)\n", "\n", "consed.autoFinishMinNumberOfErrorsFixedByAnExp: 0.02\n", "! if an experiment solves fewer errors than this, it isn't worth doing\n", "! so won't be chosen. This parameter controls when Autofinish stops\n", "! choosing experiments.\n", "! (YES)\n", "\n", "consed.autoFinishRedundancy: 2.0\n", "! This number should be between 1.0 and 2.0 If you want more reads\n", "! for each area, increase the number towards 2.0 If you want fewer\n", "! reads per area, decrease it towards 1.0. This only affects\n", "! universal primer reads--not custom primer reads.\n", "!\n", "! (YES)\n", "\n", "consed.autoFinishAverageInsertSize: 1500\n", "! If a template has a forward but no reverse, when deciding whether to\n", "! allow this template for a particular primer or reverse, we need to\n", "! make an assumption of where is the end of the template. If we have\n", "! do not have enough forward/reverse pairs to determine the mean, then\n", "! this parameter is used.\n", "! (YES)\n", "\n", "consed.primersMaxInsertSizeOfASubclone: 3000\n", "! check +/- this distance from the primer for false-annealing\n", "! and check at most this distance for templates for a primer.\n", "! Thus if you have more than one library, make this the max of\n", "! all libraries.\n", "! (YES)\n", "\n", "consed.primersMaxMeltingTemp: 60\n", "! (YES)\n", "\n", "consed.primersMaxMeltingTempForPCR: 58\n", "! Note: the difference between consed.primersMaxMeltingTempForPCR and\n", "! consed.primersMinMeltingTempForPCR must be less than or equal to\n", "! consed.primersMaxMeltingTempDifferenceForPCR\n", "! Otherwise, autofinish may take forever to pick pcr primers.\n", "! (YES)\n", "\n", "consed.primersPickTemplatesForPrimers: true\n", "! when picking primers for subclone templates, pick templates also.\n", "! If there is no suitable template for a primer, do not pick the\n", "! primer. If you like to pick your own templates, you might want to\n", "! turn this off for a little improvement in speed.\n", "! This has no effect on Autofinish--just on interactive primer picking\n", "! in Consed.\n", "! (YES)\n", "\n", "consed.primersSubcloneFullPathnameOfFileOfSequencesForScreening: $CONSED_HOME/lib/screenLibs/primerSubcloneScreen.seq\n", "! vector sequence file if choosing subclone (e.g., M13, plasmid)\n", "! templates\n", "! (YES)\n", "\n", "consed.primersCloneFullPathnameOfFileOfSequencesForScreening: $CONSED_HOME/lib/screenLibs/primerCloneScreen.seq\n", "! vector sequence file if choosing clone (e.g., cosmid, BAC) template\n", "! (YES)\n", "\n", "consed.primersMinMeltingTemp: 55\n", "! (YES)\n", "\n", "consed.primersMinMeltingTempForPCR: 55\n", "! (YES)\n", "\n", "consed.searchFunctionsUseUnalignedEndsOfReads: false\n", "! when navigating by \n", "! searchForSingleSubcloneRegions and searchForSingleStrandedRegions,\n", "! and the read below has both aligned and unaligned portions, which\n", "! bases of the read are considered to cover the region:\n", "! uuuuuuuAAAAAAAAAAAAAAAAAAAAAAAAAuuuuuuuu\n", "! <--------- if \"true\" ------------------>\n", "! <-----if \"false\"-------->\n", "! where u means an unaligned base and A means an aligned base\n", "! (YES)\n", "\n", "consed.searchFunctionsUseLowQualityEndsOfReads: true\n", "! when navigating by \n", "! searchForSingleSubcloneRegions and searchForSingleStrandedRegions,\n", "! and the read below has both low quality and high quality portions,\n", "! which portions of the read are considered to cover the region:\n", "! lllllllAAAAAAAAAAAAAAAAAAAAAAAAAllllllll\n", "! <--------- if \"true\" ------------------>\n", "! <-----if \"false\"-------->\n", "! where l means a low quality base and A means a high quality base\n", "! (YES)\n", "\n", "consed.inexactSearchForStringMaxPerCentMismatch: 5\n", "! when using the inexact search for string, allow up to this\n", "! % mismatch: the sum of the insertion, deletion, and substitution\n", "! differences divided by the length of the query string\n", "! (YES)\n", "\n", "consed.onlyAllowOneReadWriteConsedAtATime: false\n", "! if there is another read-write consed (or Autofinish) process running in the\n", "! same directory, and this consed (or Autofinish) is not read-only,\n", "! then terminate with an error message\n", "! (YES)\n", "\n", "consed.autoFinishAllowHighQualityDiscrepanciesInTemplateIfConsistentForwardReversePair: true\n", "! otherwise, a single serious hqd will cause the template to be rejected.\n", "! (YES)\n", "\n", "\n", "consed.printWindowCommand: /usr/bin/X11/xwd | /usr/bin/X11/xpr | /bin/lp -dlevulose\n", "! system command to print out a Consed Window\n", "! (YES)\n", "\n", "consed.fileOfTagTypes:\n", "! pathname of a file with the following format:\n", "! (tag name) (color for displaying) (consensus or read or both) (yes/no)\n", "! where \"consensus\" or \"read\" or \"both\" indicates whether the tag\n", "! is available for the user to add to the consensus, to reads, or to\n", "! both, and \"yes\" or \"no\" indicates whether the tag can be created\n", "! in Consed by swiping, or whether it only can be created by an\n", "! external program and displayed by Consed.\n", "! (YES)\n", "\n", "consed.assemblyViewShowConsistentFwdRevPairs: false\n", "! too many squares! See assemblyViewShowConsistentFwdRevPairDepth\n", "! (YES)\n", "\n", "consed.assemblyViewShowConsistentFwdRevPairDepth: false\n", "! This actually shows more information than \n", "! assemblyViewShowConsistentFwdRevPairs and is much easier to read\n", "! (YES)\n", "\n", "consed.assemblyViewShowConsistentFwdRevPairsBetweenDifferentScaffolds: true\n", "! Lone links from the end of one contig to the end of another, but not\n", "! confirmed by another in order to make the contigs joined into a scaffold.\n", "! (YES)\n", "\n", "consed.assemblyViewShowLegsOnSquaresForConsistentFwdRevPairs: false\n", "! This is even more cluttered than assemblyViewShowConsistentFwdRevPairs\n", "! (YES)\n", "\n", "consed.assemblyViewShowGapSpanningFwdRevPairs: true\n", "! This shows gap-spanning fwd/rev pairs that caused the contigs to\n", "! be joined into a scaffold.\n", "! (YES)\n", "\n", "consed.assemblyViewShowWhichInconsistentFwdRevPairs: filtered\n", "! choices are: filtered, none, all\n", "! \"filtered\" means that an inconsistent fwd/rev pair is only shown\n", "! if it is confirmed by another inconsistent fwd/rev pair\n", "! If all, full of red lines. If filtered, then only red lines that are\n", "! confirmed by other red lines are shown.\n", "! (YES)\n", "\n", "consed.assemblyViewShowReadDepth: true\n", "! If true, read depth is shown in assemblyView\n", "! (YES)\n", "\n", "consed.assemblyViewShowMultipleHighQualityDiscrepancies: false\n", "! If true, multiple high quality discrepancies (both indel and\n", "! non-indel type) are shown in assemblyView\n", "! (YES)\n", "\n", "consed.assemblyViewShowRestrictionDigestCutSites: true\n", "! If true, and you open a Digest Window in Consed and you open\n", "! the Assembly View window in Consed, the restriction digest cut\n", "! sites will be shown in Assembly View (in addition to showing them in \n", "! the Digest Window)\n", "! (YES)\n", "\n", "consed.assemblyViewFilterSequenceMatchesBySize: false\n", "! only show sequence matches if they fall between\n", "! consed.assemblyViewSequenceMatchesMinSize and\n", "! consed.assemblyViewSequenceMatchesMaxSize\n", "! (YES)\n", "\n", "consed.assemblyViewSequenceMatchesMinSize: 100\n", "! if consed.assemblyViewFilterSequenceMatchesBySize is true,\n", "! then only show sequence matches that are larger than this\n", "! (YES)\n", "\n", "consed.assemblyViewSequenceMatchesMaxSize: 10000\n", "! if consed.assemblyViewFilterSequenceMatchesBySize is true,\n", "! then only show sequence matches that are smaller than this\n", "! (YES)\n", "\n", "consed.assemblyViewAutomaticallyStartWithConsed: false\n", "! when consed starts, start assembly view. This only works if you\n", "! specify the ace file on the command line.\n", "! (YES)\n", "\n", "consed.assemblyViewDisplayTheseTagTypesOnTheseLines: edit 0 matchElsewhereHighQual 1 matchElsewhereLowQual 2\n", "! space-separated list of form:\n", "! (tagtype) (line number) (tagtype) (line number)\n", "! where line number is where in Assembly View the tag will be displayed\n", "! (YES)\n", "\n", "consed.assemblyViewShowTags: true\n", "! If true, and some tag types are selected, these tags\n", "! will be shown in assemblyView. If false, no tags\n", "! will be shown in assemblyView.\n", "! (YES)\n", "\n", "consed.autoEditRecalculateHighQualitySegmentsOfReads: false\n", "! If true, will recalculate the high quality segments of the reads\n", "! (YES)\n", "\n", "consed.autoEditConvertCloneEndBasesToXs: true\n", "! If true, will convert to X's bases of all reads that protrude beyond a\n", "! cloneEnd tag.\n", "! (YES)\n", "\n", "consed.autoEditTellPhrapNotToOverlapMultiplyDiscrepantReads: true\n", "! This will find all locations where there are multiple identical \n", "! discrepancies with the consensus (and some other conditions) and try\n", "! to make most of the reads quality 99 at that location so that phrap,\n", "! next time it is run, will not overlap those reads. This will fix\n", "! many misassemblies.\n", "! (YES)\n", "\n", "consed.autoEditTagEditableLowConsensusQualityRegions: true\n", "! This will find regions that are low quality, but that a human\n", "! finisher could easily determine the correct base and thus\n", "! money could be saved by not having Autofinish suggest additional\n", "! reads overlapping the region\n", "! (YES)\n", "\n", "consed.autoEditMakeFakeRead: false\n", "! takes a list of reads and makes a false read that consists of the\n", "! combination of those reads (using the consensus to fill in between\n", "! them)\n", "! (YES)\n", "\n", "consed.autoEditMakeFakeReadFromRead1: read1\n", "! read 1 from which to make the fake read\n", "\n", "consed.autoEditMakeFakeReadFromRead2: read2\n", "! read 2 from which to make the fake read\n", "\n", "consed.autoEditMakeFakeReadName: mama\n", "! name of fake read\n", "\n", "consed.autoEditMakeFakeReadFastaFilename: mama.fa\n", "! name of fasta file to put the read into\n", "\n", "consed.autoEditMergeAssembly: false\n", "! This is used to take 2 assemblies (each with a single contig) that\n", "! have a read in common and merge them into a single assembly with a\n", "! single contig as follows: It reads consed.autoEditSecondaryAceFile\n", "! into a secondary assembly and finds read\n", "! consed.autoEditMakeFakeReadName within that secondary assembly as well\n", "! as within the primary assembly. It assumes that these reads have the\n", "! same unpadded bases (although they may have different pads). It\n", "! equalizes the pads, and then moves the other reads (which are\n", "! typically the fwd/rev pair of reads) from the secondary assembly into\n", "! the primary assembly. It then deletes the secondary assembly and\n", "! deletes consed.autoEditMakeFakeReadName from the primary assembly.\n", "! (YES)\n", "\n", "consed.autoEditSecondaryAceFile: mama.ace\n", "! ace file of the fake read and the forward/reverse pair\n", "\n", "consed.autoEditFixRunsInConsensus: false\n", "! fixes this: \n", "! ccc (cons)\n", "! cc* (read1)\n", "! *cc (read2)\n", "! (YES) \n", "\n", "consed.showAllTracesJustShowGoodTraces: true\n", "! Just show traces where there is a base at the cursor and\n", "! there is trace signal at the cursor and where \n", "! there is no \"dataNeeded\" tag at the cursor as specified by\n", "! consed.showAllTracesDoNotShowTraceIfTheseTagsPresent\n", "! (YES)\n", "\n", "consed.addAlignedSequenceQualityOfBases: 40\n", "! when running consed -addAlignedSequence, what quality should the\n", "! bases be?\n", "! (YES)\n", "\n", "consed.makeLightBackgroundInAlignedReadsWindowAndTracesWindow: false\n", "! for printing screens, saves toner\n", "! (YES)\n", "\n", "consed.putVerticalLineAtCursor: true\n", "! for very high depth of coverage regions, a line helps your eye see\n", "! follow the column\n", "! (YES)\n", "\n", "consed.putHorizontalLineAtCursor: true\n", "! for very wide monitors, helps to follow a read with your eye\n", "! (YES)\n", "\n", "consed.highlightedReadsFile: highlighted_reads.txt\n", "! The user can use the \"Misc/save highlighted reads to file\" function\n", "! to save highlighted read names to this file.\n", "! (YES)\n", "\n", "!\n", "!\n", "! parameters in the (OK) category:\n", "!\n", "!\n", "!\n", "\n", "consed.autoReportPrintReadNamesInRegion: false\n", "!(OK)\n", "\n", "consed.autoReportPrintReadNamesInRegionContig: Contig1\n", "!(OK)\n", "\n", "consed.autoReportPrintReadNamesInRegionLeftPos: 1\n", "!(OK)\n", "\n", "consed.autoReportPrintReadNamesInRegionRightPos: 1000\n", "!(OK)\n", "\n", "consed.autoReportPrintHighlyDiscrepantRegions: false\n", "! motivated by solexa reads. Print where many reads disagree with\n", "! reference sequence\n", "! uses: \n", "! consed.qualityThresholdForFindingHighQualityDiscrepancies\n", "! ignores bases lower than this\n", "! consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads\n", "! consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage\n", "! consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality\n", "! consed.navigateByHighlyDiscrepantPositionsJustListIndels\n", "! consed.navigateByHighlyDiscrepantPositionsIgnoreIfNOrXInConsensus: false\n", "! (OK)\n", "\n", "consed.autoReportPrintScaffolds: false\n", "! (OK)\n", "\n", "consed.numberUnpaddedConsensusAtUserDefined: true\n", "! allow user to put a tag on the consensus to specify the number to\n", "! start numbering the consensus.\n", "! Must use tag consed.tagColorStartNumberingConsensus as the\n", "! tag with the number in it.\n", "! (OK)\n", "\n", "consed.autoReportPrintHighQualityDiscrepancies: false\n", "! (OK)\n", "\n", "consed.autoReportHighQualityDiscrepanciesExcludeCompressionOrG_dropoutTags: true\n", "! used in connection with consed.autoReportPrintHighQualityDiscrepancies\n", "! (OK)\n", "\n", "consed.autoReportHighQualityDiscrepanciesExcludeMostPads: true\n", "! used in connection with consed.autoReportPrintHighQualityDiscrepancies\n", "! Excludes high quality discrepancy pads except those in cases such as this:\n", "! consensus aa\n", "! read 1 *a\n", "! read 2 *a\n", "! read 3 a*\n", "! read 4 a*\n", "! (OK)\n", "\n", "consed.autoReportPrintLowConsensusQualityRegions: false\n", "! (OK)\n", "\n", "consed.autoReportPrintSingleSubcloneRegions: false\n", "! (OK)\n", "\n", "consed.autoReportPrintSingleStrandedRegions: false\n", "! (OK)\n", "\n", "consed.autoReportPrintLinkingForwardReversePairs: false\n", "! (OK)\n", "\n", "consed.autoReportPrintFilteredInconsistentForwardReversePairs: false\n", "! (OK)\n", "\n", "consed.autoReportPrintAssemblySummary: false\n", "! (OK)\n", "\n", "consed.showAllTracesDoNotShowTraceIfTheseTagsPresent: dataNeeded \n", "! See consed.showAllTracesJustShowGoodTraces \n", "! (OK)\n", "\n", "consed.nameOfFakeJoiningReadsIncludesAceFileName: false\n", "! This is useful if the user is going to combine the reads\n", "! from a number of different ace files together. \n", "! (OK)\n", "\n", "consed.whenUserScrollsOffWindowMillisecondsBetweenScrolling: 250\n", "! (OK)\n", "\n", "consed.whenUserScrollsOffWindowBasesToScrollEachTime: 15\n", "! (OK)\n", "\n", "consed.compareContigsUseBandedRatherThanFullSmithWaterman: true\n", "! (OK)\n", "\n", "consed.compareContigsBandSize: 50\n", "! band size of banded Smith Waterman\n", "! (OK)\n", "\n", "consed.assemblyViewShowFwdRevPairDepthsInRedIfOnlyThisMany: 1\n", "! (OK)\n", "\n", "consed.assemblyViewShowSequenceMatches: true\n", "! When false, do not show any sequence matches (repeats) \n", "! at all in Assembly View.\n", "! Some people like to start out this way since displaying sequence\n", "! matches slows down scrolling.\n", "! (OK)\n", "\n", "consed.assemblyViewOKToShowSequenceMatchesBetweenContigs: true\n", "! (OK)\n", "\n", "consed.assemblyViewOKToShowSequenceMatchesWithinContigs: true\n", "! (OK)\n", "\n", "consed.assemblyViewOKToShowDirectSequenceMatches: true\n", "! This means in which neither copy must be complemented with respect\n", "! to the way it is in the scaffold as created by Consed.\n", "! (OK)\n", "\n", "consed.assemblyViewOKToShowInvertedSequenceMatches: true\n", "! This means that exactly one copy must be complemented with respect\n", "! to the way it is in the scaffold as created by Consed.\n", "! (OK)\n", "\n", "consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion: false\n", "! You must set consed.assemblyViewOnlyShowSequencematchesToThisContig\n", "! consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft\n", "! consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight\n", "! (OK)\n", "\n", "consed.assemblyViewOnlyShowSequenceMatchesToThisContig:\n", "! You must make\n", "! consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion: true\n", "! (OK)\n", "\n", "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionLeft: 0\n", "! consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion: true\n", "! (OK)\n", "\n", "consed.assemblyViewOnlyShowSequenceMatchesToThisRegionRight: 0\n", "! consed.assemblyViewOnlyShowSequenceMatchesToAParticularRegion: true\n", "! (OK)\n", "\n", "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigs: false\n", "! (OK)\n", "\n", "consed.assemblyViewOnlyShowSequenceMatchesToEndsOfContigsThisFar: 1000\n", "! This many base pairs from the end of the contig.\n", "! (OK)\n", "\n", "consed.defaultReadPrefix: *\n", "! This is used as the character to prefix reads with when the \n", "! read is in consed.readPrefixesFile and the prefix is not specified.\n", "! (OK)\n", "\n", "consed.readPrefixesFile: readPrefixes.txt\n", "! This file should contain a list of reads that you would want to \n", "! have prefixes in the Aligned Reads Window. Each line should\n", "! have the following format:\n", "! (read name) (prefix) (color)\n", "! The prefix and color are optional. You can have a line like this:\n", "! (read name) (prefix)\n", "! or this:\n", "! (read name)\n", "! but not this:\n", "! (read name) (color)\n", "! If the color is not specified, the color will default to \n", "! consed.colorReadPrefixes: blue\n", "! If the prefix is not specified, it will default to \n", "! (OK)\n", "\n", "consed.maxCharsDisplayedForReadPrefix: 1\n", "! It is still ok to have long read prefixes in the file\n", "! consed.readPrefixesFile but only this many characters\n", "! will be displayed in the Aligned Reads window\n", "! (OK)\n", "\n", "consed.autoFinishDoNotDoPCRIfThisManyAvailableGapSpanningTemplates: 2\n", "! (OK)\n", "\n", "consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions: 6\n", "! \"unoriented\" pcr reactions means cases in which autofinish is suggesting\n", "! a pcr reaction to span a gap, but it doesn't know whether the 2 contig ends\n", "! really go together since there are not enough (or no)templates that span \n", "! that gap \n", "! (OK)\n", "\n", "consed.autoFinishDoNotDoOrientedPCRIfGapSizeLargerThanThis: 10000\n", "! Gap size can be specified in user-defined contigEndPair tags in a \n", "! gap_size: field\n", "! If the gap size is greater than this number, do not do PCR.\n", "! (OK)\n", "\n", "consed.autoFinishDoNotDoPCRIfEndIsExtendedByReads: false\n", "! If this is true, and autofinish was able to walk off the end of a\n", "! contig, do not do PCR with that end of the contig. \n", "!\n", "! (OK)\n", "\n", "consed.autoFinishMaxAcceptableErrorsPerMegabase: 0\n", "! target error rate. This parameter used to be the one that stopped\n", "! Autofinish from calling more reads. However, consider a BAC that is\n", "! nearly perfect except for one region with 3 quality 10 bases in a\n", "! row. In this case the global errors per megabase is very\n", "! low--perhaps lower than 1 error per megabase. Despite this, most\n", "! labs would like to do one more read to fix this problem. Thus we\n", "! set this parameter to zero (to disable it) so Autofinish will use\n", "! the parameter consed.autoFinishMinNumberOfErrorsFixedByAnExp to stop\n", "! calling more reads--it is a local error rate.\n", "! (OK)\n", "\n", "consed.autoFinishIfNotEnoughFwdRevPairsUseThisPerCentOfInsertSize: 90\n", "! If a template has a forward but no reverse, when deciding whether to\n", "! allow this template for a particular primer, we need to make an assumption\n", "! of where is the end of the template. If the template comes from a library\n", "! with insert size 1500, it would be reasonable to assume that the end of\n", "! template will be 1500 bases from the forward read. But if this template\n", "! has an insert that is shorter than average, the walk may walk into vector.\n", "! To be conservative, we may want to assume that the insert is somewhat \n", "! shorter than average. By default, we assume that it is 90% as large as \n", "! the average. This parameter gives that percentage. This parameter\n", "! is used both by Consed and Autofinish.\n", "! (OK)\n", "\n", "consed.primersNumberOfBasesToBackUpToStartLooking: 50\n", "! e.g., if this is 50 and you want a read at position 1000, primers\n", "! will be searched before base 950 but not in the region 950 to 1000\n", "! This has no effect on Autofinish--just on interactively picking primers.\n", "! (OK)\n", "\n", "consed.primersMakePCRPrimersThisManyBasesBackFromEndOfHighQualitySegment: 100\n", "! When a PCR product is made, you want it to overlap by this many bases\n", "! the high quality part of the existing consensus. Thus choose PCR\n", "! primers this many bases back (or more)\n", "! (OK)\n", "\n", "consed.primersOKToChoosePrimersInSingleSubcloneRegion: true\n", "! (OK)\n", "\n", "consed.primersOKToChoosePrimersWhereHighQualityDiscrepancies: false\n", "! (OK)\n", "\n", "consed.primersOKToChoosePrimersWhereUnalignedHighQualityRegion: false\n", "! (OK)\n", "\n", "consed.autoFinishCallReversesToFlankGaps: true\n", "! if there is a forward-reverse pair flanking a gap, print it out\n", "! if there is not, suggest reverses to flank the gap\n", "! (OK)\n", "\n", "consed.autoFinishAllowWholeCloneReads: false\n", "! ok to call reads whose template for sequencing reaction is the\n", "! entire clone (BAC or cosmid)\n", "! (OK)\n", "\n", "consed.autoFinishAllowCustomPrimerSubcloneReads: true\n", "! ok to call reads with custom primers and subclone template\n", "! (OK)\n", "\n", "consed.autoFinishAllowResequencingReads: true\n", "! This is just universal primer reads to be resequenced using\n", "! dye terminator chemistry or special chemistry. (It does not\n", "! mean resequencing a custom primer read.)\n", "! (OK)\n", "\n", "consed.autoFinishAllowResequencingReadsOnlyForRunsAndStops: false\n", "! This parameter only has any effect when\n", "! consed.autoFinishAllowResequencingReads is set to true. In that\n", "! case no resequencing reads will be suggested, unless it is to cross\n", "! a run or stop and special chemistry is suggested.\n", "! (OK) \n", "\n", "consed.autoFinishAllowDeNovoUniversalPrimerSubcloneReads: true\n", "! Allows calling reverse when there is just a forward.\n", "! Allows calling a forward when there is just a reverse.\n", "! (OK)\n", "\n", "consed.autoFinishAllowMinilibraries: false\n", "! Allows calling minilibraries (shatter libraries or transposon\n", "! libraries) of subclone templates for closing gaps\n", "! (OK)\n", "\n", "consed.autoFinishAllowPCR: true\n", "! Allows calling PCR for closing gaps, but only as a last resort\n", "! (OK)\n", "\n", "consed.autoFinishAllowUnorientedPCRReactions: true\n", "! Allows calling PCR amongst contig-ends that have insufficient\n", "! fwd/rev pair linkage to any other contig-end. Thus it suggests\n", "! pcr amongst all such contig-ends. \n", "! To allow this type of pcr, you must also make:\n", "! consed.autoFinishAllowPCRForUnorientedContigEnds: true\n", "! See also:\n", "! consed.autoFinishDoNotDoUnorientedPCRIfThisManyOrMoreUnorientedPCRReactions: \n", "! which gives you finer control over unoriented pcr.\n", "! (OK)\n", "\n", "consed.autoFinishAllowResequencingAUniversalPrimerAutofinishRead: false\n", "! if Autofinish suggests a de novo universal primer read,\n", "! do not allow Autofinish to suggest a resequence of this read\n", "! (OK)\n", "\n", "\n", "consed.autoFinishAlwaysCloseGapsUsingMinilibraries: false\n", "! \"Minilibraries\" includes transposing a subclone template or\n", "! making a shatter library from a subclone template\n", "! (OK)\n", "\n", "consed.autoFinishMaximumFinishingReadLength: 2000\n", "! Change this only if your finishing reads are typically shorter\n", "! than your shotgun reads. Otherwise, leave it unrealistically long,\n", "! and Autofinish will set its model read based on your existing\n", "! shotgun reads.\n", "! (OK)\n", "\n", "consed.autoFinishSuggestMinilibraryIfGapThisManyBasesOrLarger: 800\n", "! (OK)\n", "\n", "consed.autoFinishSuggestSpecialChemistryForRunsAndStops: true\n", "! Suggest special chemistry such as dGTP for reads that cross\n", "! mononucleotide or dinucleotide repeats that cause reads to fail or \n", "! stops (structure) that cause reads to fail and thus dye terminator\n", "! reads won't work.\n", "! (OK)\n", "\n", "\n", "consed.autoFinishSuggestThisManyMinilibrariesPerGap: 2\n", "! (OK)\n", "\n", "consed.primersWindowSizeInLooking: 450\n", "! e.g., if this is 300, with example above, primers will be searched\n", "! from base 650 to 950. This has no effect on Autofinish--it is just\n", "! used for interactive primer picking in Consed.\n", "! (OK)\n", "\n", "consed.primersAssumeTemplatesAreDoubleStrandedUnlessSpecified: false\n", "! you can put the template type in the phd file in a WR template item\n", "! consed will have a list of these and know which are single and\n", "! double stranded\n", "! (OK)\n", "\n", "consed.alignedReadsWindowInitialCharsWide: 60\n", "! initial width of the aligned reads window including the read name and \n", "! the bases\n", "! (OK)\n", "\n", "consed.alignedReadsWindowInitialCharsHigh: 20\n", "! initial height of the aligned reads window area where the consensus\n", "! and reads are\n", "! (OK)\n", "\n", "consed.alignedReadsWindowMaxCharsForReadNames: 20\n", "! how many columns are reserved for read names\n", "! (OK)\n", "\n", "consed.alignedReadsWindowAutomaticallyExpandRoomForReadNames: true\n", "! If true, expand and contract space for read names, but don't\n", "! contract less than consed.alignedReadsWindowMaxCharsForReadNames.\n", "! If false, then always use\n", "! consed.alignedReadsWindowMaxCharsForReadNames\n", "! for space reserved for read names.\n", "! (OK)\n", "\n", "consed.autoFinishAllowResequencingReadsToExtendContigs: false\n", "! if false, a resequencing read is not called to extend a contig--only\n", "! custom primer reads and de novo universal primer reads are called\n", "! for this purpose. \n", "! (OK)\n", "\n", "consed.autoFinishCallHowManyReversesToFlankGaps: 2\n", "! This has two purposes: 1) it specifies how many forward/reverse\n", "! pairs should be present for Consed/Autofinish to be certain of the\n", "! order/ orientation of two contigs. If there are this many fwd/rev\n", "! pairs flanking a gap, Autofinish will print out the contig ends that\n", "! flank the gap. 2) If consed.autoFinishCallReversesToFlankGaps is\n", "! set to true, and there are less than this many fwd/rev pairs\n", "! flanking a gap, Autofinish will suggest additional reverses until\n", "! there are this many.\n", "! (OK)\n", "\n", "consed.autoFinishCloseGaps: true\n", "! this allows you to turn off choosing reads to close gaps\n", "! (OK)\n", "\n", "consed.autoFinishContinueEvenThoughReadInfoDoesNotMakeSense: false\n", "! this allows you to override the checks that autofinish makes on the\n", "! read info, such as checking there are not more than 5 or so reads\n", "! from the same subclone template\n", "! (OK)\n", "\n", "consed.autoFinishCostOfResequencingUniversalPrimerSubcloneReaction: 20.0\n", "! compares universal primer subclone reaction, custom primer subclone \n", "! reaction, and custom primer clone reaction to decide which to favor\n", "! (OK)\n", "\n", "consed.autoFinishCostOfCustomPrimerSubcloneReaction: 60.0\n", "! see above\n", "! (OK)\n", "\n", "consed.autoFinishCostOfCustomPrimerCloneReaction: 80.0\n", "! see above \n", "! (OK)\n", "\n", "consed.autoFinishCostOfDeNovoUniversalPrimerSubcloneReaction: 60.0\n", "! cost of reverse where there is only a forward or cost of forward\n", "! when there is only a reverse\n", "! (OK)\n", "\n", "consed.autoFinishCostOfMinilibrary: 500.0\n", "! cost of making a minilibrary (transposon library or shatter library)\n", "! from a subclone template\n", "! (OK)\n", "\n", "consed.autoFinishCoverSingleSubcloneRegions: true\n", "! this allows you to turn off choosing reads to cover single subclone regions\n", "! (OK)\n", "\n", "consed.autoFinishCoverLowConsensusQualityRegions: true\n", "! this allows you to turn off choosing reads to cover low consensus\n", "! quality regions\n", "! (OK)\n", "\n", "consed.autoFinishDebugUniversalPrimerReadsFile: gordon_debug.txt\n", "! for debugging Autofinish\n", "! put a file with this name in the same directory as the ace file\n", "! format:\n", "! fcalld09 fwd\n", "! fgj74f01 rev\n", "! (template name) (fwd or rev)\n", "! (OK)\n", "\n", "consed.autoFinishDebugCustomPrimerReadsFile: debug_custom.txt\n", "! for debugging Autofinish\n", "! put a file with this name in the same directory as the ace file\n", "! format:\n", "! cgggacctgg\n", "! (primer in 5' to 3' orientation)\n", "! (OK)\n", "\n", "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases: 200\n", "! see consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether\n", "! (OK)\n", "\n", "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloserThanThisManyBases: 300\n", "! see consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether\n", "! (OK)\n", "\n", "consed.autoFinishDoNotFinishWhereTheseTagsAre: doNotFinish editable\n", "! list of tag types separated by spaces. E.g.,\n", "! doNotFinish repeat \n", "! tells autofinish that you are not interested in finishing in this region\n", "! (OK)\n", "\n", "consed.autoFinishDoNotExtendContigsWhereTheseTagsAre: doNotFinish\n", "! list of tag types separated by spaces. E.g.,\n", "! doNotFinish repeat\n", "! tells autofinish that you do not want to extend the contig near this\n", "! tag. If you do not want this feature, just leave the list empty.\n", "! (OK)\n", "\n", "consed.autoFinishDoNotExtendContigsIfTagsAreThisCloseToContigEnd: 50\n", "! Uses the list from consed.autoFinishDoNotExtendContigsWhereTheseTagsAre\n", "! and checks if any of these tags are within this many bases of the end of \n", "! the contig. If they are, does not extend the contig.\n", "! (OK)\n", "\n", "consed.dumpContigOrderAndOrientationInfoToThisFile:\n", "! In the case of Consed (not autofinish or autoPCRAmplify), send the\n", "! output to this file rather than stderr. If this name is blank, \n", "! continue (in case of consed), to send output to stderr.\n", "! (OK)\n", "\n", "consed.autoFinishDumpTemplates: false\n", "! for debugging, this allows you to dump all information about the \n", "! templates--insert locations \n", "! (OK)\n", "\n", "consed.autoFinishExcludeContigIfOnlyThisManyReadsOrLess: 10\n", "! (OK)\n", "\n", "consed.autoFinishExcludeContigIfDepthOfCoverageGreaterThanThis: 50.0\n", "! To exclude contigs that are probably E. coli contamination\n", "! \"depth of coverage\" is defined here to mean the sum of the read\n", "! lengths (including low quality ends) divided by the contig length.\n", "! (OK)\n", "\n", "consed.autoFinishExcludeContigIfThisManyBasesOrLess: 1000\n", "! consed.autoFinishExcludeContigIfTooShort must be set to true for\n", "! this to have any effect\n", "! (OK)\n", "\n", "consed.autoFinishHowManyTemplatesYouIntendToUseForCustomPrimerSubcloneReactions: 3\n", "! this tells autofinish which templates you are planning on using\n", "! which is necessary to figure out which regions will still be single\n", "! subclone regions\n", "! (OK)\n", "\n", "\n", "consed.primersMinNumberOfTemplatesForPrimers: 1\n", "! if there are fewer templates than this, the primer is rejected\n", "\n", "consed.autoFinishMinBaseOverlapBetweenAReadAndHighQualitySegmentOfConsensus: 70\n", "! when extending the consensus, a read that is too far from the\n", "! consensus will not be assembled by phrap with this contig and thus\n", "! will not be useful for extending the consensus. This gives the\n", "! minimum overlap of a read with the high quality segment of the\n", "! consensus. As reads are picked, then additional reads may be picked\n", "! further out.\n", "! (OK)\n", "\n", "consed.autoFinishNumberOfVectorBasesAtBeginningOfAUniveralPrimerRead: 40\n", "! used to figure out where the beginning of a reverse will be. Not\n", "! important to be accurate because the insert size is so uncertain\n", "! (OK)\n", "\n", "consed.autoFinishCDNANotGenomic: false\n", "! If this is set to true, the whole clone is assumed to be cDNA and,\n", "! rather than the normal method of detecting the end of the clone,\n", "! Autofinish detects the end of the cDNA as follows:\n", "! the user is expected to add whole read items of type 'template',\n", "! with 'type: univ fwd' for the 5' end and 'type: univ rev' for the 3'\n", "! end of the cDNA. \n", "! (OK)\n", "\n", "consed.autoFinishConfidenceThatReadWillCoverSingleSubcloneRegion: 90\n", "! Autofinish computes the per cent of existing reads are aligned at\n", "! each base position. Typically, this number starts at around 0% at\n", "! base position 1, rises to close to 100% at around base position 300,\n", "! and then drops again to 0% at base position 800 or so. This number\n", "! specifies how high the number must be for Autofinish to consider an\n", "! Autofinish read to cover a single subclone region.\n", "! (OK)\n", "\n", "consed.autoFinishPrintForwardOrReverseStrandWhenPrintingSubcloneTemplatesForCustomPrimerReads: true\n", "! If this is true, then custom primer reads are printed out like this:\n", "! tccagaaaactaattcaaaataatg,56,standard.2,->,2413,2413,3681,Contig1,9,djs74_690 (fwd),10,djs74_1803 (fwd),11,djs74_1861 (fwd)\n", "! If this is false, then custom primer reads are printed out like this:\n", "! tccagaaaactaattcaaaataatg,56,standard.2,->,2413,2413,3681,Contig1,9,djs74_690,10,djs74_1803,11,djs74_1861\n", "! The difference is the (fwd) or (rev) that indicates which strand of\n", "! the subclone template is to be used. This is particularly important if\n", "! you use M13 and thus must make the reverse strand.\n", "! (OK)\n", "\n", "consed.autoFinishPrintMinilibrariesSummaryFile: false\n", "! If this is true, Autofinish will print a file with name\n", "! xxx.minilibraries just as it prints one as xxx.univReverses and\n", "! xxx.univForwards\n", "! (OK)\n", "\n", "consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs: true\n", "! This is set to true to increase the chance of closing a gap. For\n", "! every subclone template that has just one universal primer read\n", "! (either just a forward or just a reverse) that might protrude off\n", "! the end of the contig, Autofinish suggests the universal primer read\n", "! off the opposite end of the subclone template.\n", "! If this parameter is set false, then\n", "! Autofinish may still choose some of these reads, but it won't\n", "! necessarily choose them all.\n", "! (OK)\n", "\n", "consed.autoFinishDoNotIgnoreLCQIfThisManyBasesFromEndOfContigForLCQTagger: 300\n", "! Do not ignore low consensus quality bases if they are this many \n", "! bases from the end of the contig. \n", "! (OK)\n", "\n", "consed.checkIfTooManyWalks: true\n", "! this just checks if the number of walks, pcr ends, and unknown reads\n", "! exceeds 20% of the total number of reads. If this is exceeded, then \n", "! a warning message is given. Typically, such a warning indicates\n", "! that you have incorrectly customized determineReadTypes.perl\n", "! (OK)\n", "\n", "consed.numberOfColumnsBeforeReadNameInAlignedReadsWindow: 1\n", "! this is for displaying information about the whole read items, \n", "! both from PHD files and from a file\n", "\n", "consed.compareContigsAlignsThisManyBasesMax: 2000\n", "! (OK)\n", "\n", "consed.compressedChromatExtension: .gz\n", "! (OK)\n", "\n", "consed.dimLowQualityEndsOfReads: false\n", "!\n", "! (OK)\n", "\n", "\n", "consed.dimUnalignedEndsOfReads: true\n", "! (OK)\n", "\n", "consed.fakeReadsSpecifiedByFilenameExtension: true\n", "! if this is true, then reads that end with .a[0-9]* or .c[0-9]* will\n", "! be considered fake reads. Otherwise, fake reads will be indicated\n", "! by a WR item in the PHD file.\n", "! (OK)\n", "\n", "consed.fullPathnameOfAddReads2ConsedScript: $CONSED_HOME/bin/addReads2Consed.perl\n", "! (OK)\n", "\n", "consed.fullPathnameOfFixContigEndScript: $CONSED_HOME/bin/fixContigEnd.perl\n", "! (OK)\n", "\n", "consed.fixContigEndsCleanUpTemporaryFiles: true\n", "! -fixContigEnds leaves behind zillions of temporary files from\n", "! phrapping. Delete these (except for debugging).\n", "! (OK)\n", "\n", "consed.fixContigEndsMinSmithWatermanScoreToMakeJoin: 30\n", "! when making the join, if the smith-waterman score is less\n", "! than this, do not make the join and leave the contig-end as is\n", "! (NO)\n", "\n", "consed.fixContigEndsMinNumberOfReadsInContig: 5\n", "! only fix contigs that have this number of reads or more\n", "! (YES)\n", "\n", "consed.fullPathnameOfCrossMatch: $CONSED_HOME/bin/cross_match\n", "! (OK)\n", "\n", "consed.fullPathnameOfPhred: $CONSED_HOME/bin/phred\n", "! (OK)\n", "\n", "consed.fullPathnameOfMiniassemblyScript: $CONSED_HOME/bin/phredPhrap\n", "! If you are up-to-date with phredPhrap, this script serves both\n", "! the purpose of assemblying the entire project, as well as making\n", "! miniassemblies. The difference is whether phredPhrap has the\n", "! -include_chromats option.\n", "! (OK)\n", "\n", "consed.gunzipFullPath: /bin/gunzip\n", "! (OK)\n", "\n", "consed.fullPathnameOfFilter454ReadsScript: $CONSED_HOME/bin/filter454Reads.perl\n", "! Runs crossmatch between the unpaired reads and puc19 to eliminate those\n", "! reads contaminated with puc19\n", "! (OK)\n", "\n", "consed.filter454ReadsAgainstThis: $CONSED_HOME/lib/screenLibs/filter454Reads.fa\n", "! used by consed.fullPathnameOfFilter454ReadsAgainstVectorScript\n", "! (OK)\n", "\n", "consed.454LinkerSequences: $CONSED_HOME/lib/screenLibs/sffLinkers.fa\n", "! the linker sequence for paired-end 454 reads used in \n", "! sff2PhdBall\n", "! (OK)\n", "\n", "consed.hideSomeTagTypesAtStartup: false\n", "! (OK)\n", "\n", "consed.maximumNumberOfTracesShown: 4\n", "! (OK)\n", "\n", "consed.navigateAutomaticTracePopup: false\n", "! (OK)\n", "\n", "consed.navigateAutomaticAllTracesPopup: false\n", "! (OK)\n", "\n", "consed.primersMinimumLengthOfAPrimer: 15\n", "! (OK)\n", "\n", "consed.primersMaximumLengthOfAPrimer: 25\n", "! (OK)\n", "\n", "consed.primersMinimumLengthOfAPrimerForPCR: 18\n", "! (OK)\n", "\n", "consed.primersMaximumLengthOfAPrimerForPCR: 30\n", "! (OK)\n", "\n", "consed.primersMaxMeltingTempDifferenceForPCR: 3.0\n", "! how large can the difference of melting temperatures be between\n", "! two primers of a PCR primer pair\n", "! (OK)\n", "\n", "consed.primersMaxPCRPrimerPairsToDisplay: 100000\n", "! there is a limit here, because there could possibly be millions\n", "! (OK)\n", "\n", "consed.primersCheckJustSomePCRPrimerPairsRatherThanAll: true\n", "! If there are 1000 1st primers, and 1000 2nd primers, that gives\n", "! a million pairs for Consed to check, which takes a long time. So\n", "! instead, just check some of the pairs\n", "! (OK)\n", "\n", "consed.primersNumberOfTemplatesToDisplayInFront: 2\n", "! this shows the number of templates to show in the interactive primer\n", "! picking window\n", "! (OK)\n", "\n", "consed.primersMaxLengthOfMononucleotideRepeat: 4\n", "! (OK)\n", "\n", "consed.primersBadLibrariesFile: badLibraries.txt\n", "! file of libraries, one per line\n", "! If any template is from any one of these libraries, then\n", "! consed/autofinish will not use this template for walking or\n", "! suggesting any universal primer reads\n", "! (OK)\n", "\n", "consed.primersLibrariesInfoFile: librariesInfo.txt\n", "! file of libraries, with one entry for each library of the following\n", "! format:\n", "! LIB{\n", "! name: library1\n", "! avgInsertSize: 3000\n", "! maxInsertSize: 5000\n", "! stranded: single\n", "! cost: 600.0\n", "! }\n", "! (OK)\n", "\n", "consed.primersBadTemplatesFile: badTemplates.txt\n", "! file of templates that you've tried, don't work, and you don't want to try\n", "! again\n", "! (OK)\n", "\n", "consed.primersChooseTemplatesByPositionInsteadOfQuality: true\n", "! Templates for subclone custom primer walks can be chosen either on\n", "! the basis of the quality of the template (as determined by the quality \n", "! of existing reads from that template) or by the location of the end of \n", "! the template. If this parameter is false, templates will be chosen\n", "! based solely on quality. If this parameter is true, then templates\n", "! with forward/reverse pairs will be picked first, followed by templates \n", "! that have the beginning of the insert closest to the primer.\n", "! (OK)\n", "\n", "consed.primersWhenChoosingATemplateMinPotentialReadLength: 350\n", "! when choosing templates for a custom primer, only choose a template\n", "! if the read can be chosen at least this long\n", "! (OK)\n", "\n", "consed.primersWindowSizeInLookingForPCR: 2000\n", "! will look this many bases back from the pointer when looking for a PCR\n", "! primer. Used both interactively and for Autofinish (see\n", "! getUnpaddedRangeForMakingPCRPrimers )\n", "! (OK)\n", "\n", "consed.qualityThresholdForFindingHighQualityDiscrepancies: 40\n", "! high quality discrepancies have this quality or higher \n", "! (OK)\n", "\n", "consed.qualityThresholdForNavigateByDepthOfCoverage: 10\n", "! for high depth of coverage, this is the minimum quality\n", "! see consed.navigateByHighDepthOfCoverageNotLow\n", "! (OK)\n", "\n", "consed.navigateByHighDepthOfCoverageNotLow: true\n", "! see consed.qualityThresholdForNavigateByDepthOfCoverage:\n", "! (OK)\n", "\n", "consed.MinDepthForNavigateByDepthOfCoverage: 10\n", "! see consed.qualityThresholdForNavigateByDepthOfCoverage:\n", "! (OK)\n", "\n", "consed.defaultVectorPathnameForRestrictionFragments: $CONSED_HOME/lib/screenLibs/singleVectorForRestrictionDigest.fasta\n", "! If you want to have the vector cut with the restriction\n", "! enzymes, put the vector sequence in a file in fasta format\n", "! and put a pathname to it here.\n", "! (OK)\n", "\n", "consed.fileOfAdditionalRestrictionEnzymes: \n", "! If you want a restriction enzyme that is not in the huge list\n", "! that comes with Consed, you can put additional enzymes in a file\n", "! and put the full pathname of that file here. The file must be in\n", "! the form:\n", "! AatI AGGCCT\n", "! where AatI is the name of the enzyme and AGGCCT is the recognized\n", "! sequence. Do not include the cut site or any other information.\n", "! There must be a single space separating them.\n", "! (OK)\n", "\n", "consed.commonRestrictionEnzymes: BglII EcoRV NsiI HindIII BamHI XhoI PstI\n", "! a space-separated list of enzymes. Make sure they match precisely\n", "! those that are either defaults or in the file indicated by\n", "! consed.fileOfAdditionalRestrictionEnzymes\n", "! (OK)\n", "\n", "consed.defaultSelectedRestrictionEnzymes: EcoRV HindIII\n", "! a space-separated list of enzymes that will initially be\n", "! selected when the user pops open the list of restriction enzymes.\n", "! Currently these must be from among the consed.commonRestrictionEnzymes\n", "! (OK)\n", "\n", "consed.restrictionEnzymesActualFragmentsFile: fragSizes.txt\n", "! format like this:\n", "! >EcoRV\n", "! 2385\n", "! 2489\n", "! -1\n", "! >XhoIII\n", "! 259\n", "! 3843\n", "! -1\n", "! (OK)\n", "\n", "consed.restrictionDigestInitialWindowSizeInTextRows: 45\n", "! (OK)\n", "\n", "consed.restrictionDigestDoNoShowAreaOfFragmentsOverThisSize: 50000\n", "! In the picture of the real and in-silico \n", "! (OK)\n", "\n", "consed.showReadsAlphabetically: false\n", "! (OK)\n", "\n", "consed.showReadsInAlignedReadsWindowOrderedByFile: false\n", "! There are now 3 different ways to sort the reads in the Aligned\n", "! Reads Window (top to bottom): \n", "! 1) alphabetically in which case you should set:\n", "! consed.showReadsAlphabetically: true \n", "! consed.showReadsInAlignedReadsWindowOrderedByFile: false\n", "! 2) by the left end of the reads in which case you should set:\n", "! consed.showReadsAlphabetically: false\n", "! consed.showReadsInAlignedReadsWindowOrderedByFile: false\n", "! 3) by a file that specifies the order of the reads in which case you\n", "! should set:\n", "! consed.showReadsAlphabetically: false\n", "! consed.showReadsInAlignedReadsWindowOrderedByFile: true\n", "! It is an error to set: \n", "! consed.showReadsAlphabetically: true\n", "! consed.showReadsInAlignedReadsWindowOrderedByFile: true\n", "! (OK)\n", "\n", "consed.showReadsInAlignedReadsWindowOrderedByThisFile: readOrder.txt\n", "! This file has one read name per line. Wildcards ('*') are allowed.\n", "! E.g.,\n", "! ABX*\n", "! myFavoriteRead.scf\n", "! *.abi\n", "! This means that all reads that start with ABX* will come first,\n", "! followed by the single read myFavoriteRead.scf and then reads that end \n", "! with .abi A read that doesn't meet any of these criteria (e.g.,\n", "! rs10469282 ) comes last. \n", "! (OK)\n", "\n", "!consed.showReadsSortedByQualityValuesAtCursor: true\n", "!bool\n", "! deprecated\n", "! Note that currently this only applies when the cursor is set\n", "! on the consensus position. When scrolling, the reads are\n", "! sorted according to consed.showReadsAlphabetically and\n", "! consed.showReadsInAlignedReadsWindowOrderedByFile\n", "! (OK)\n", "\n", "consed.showReadsAtCursorSortedHow: quality\n", "! Note that currently this only applies when the cursor is set\n", "! on the consensus position. When scrolling, the reads are\n", "! sorted according to consed.showReadsAlphabetically and\n", "! consed.showReadsInAlignedReadsWindowOrderedByFile\n", "! use the following values: quality, base, none\n", "! (OK)\n", "\n", "consed.showABIBasesInTraceWindow: false\n", "! (OK)\n", "\n", "consed.tracesWindowInitialPixelHeight: 50\n", "! (OK)\n", "\n", "consed.assemblyViewWindowInitialPixelHeight: 500\n", "! (OK)\n", "\n", "\n", "consed.assemblyViewFileOfTemplatesToNotShow: doNotShowInAssemblyView.fof\n", "! (OK)\n", "\n", "consed.assemblyViewCrossMatchMinmatch: 30\n", "! value of -minmatch to be passed to crossmatch\n", "! (OK)\n", "\n", "consed.assemblyViewCrossMatchMinscore: 60\n", "! value of -minscore to be passed to crossmatch\n", "! (OK)\n", "\n", "consed.assemblyViewFindSequenceMatchesForConsedScript: $CONSED_HOME/bin/findSequenceMatchesForConsed.perl\n", "! script that generates the file that is used by Assembly View to\n", "! show sequence matches \n", "! (OK)\n", "\n", "consed.assemblyViewCrossmatchMinmatch: 50\n", "! default value of -minmatch for running crossmatch with \n", "! findSequenceMatchesForConsed.perl\n", "! (OK)\n", "\n", "consed.assemblyViewCrossmatchMinscore: 50\n", "! default value of -minscore for running crossmatch with\n", "! findSequenceMatchesForConsed.perl\n", "! (OK)\n", "\n", "consed.assemblyViewSequenceMatchesMinimumSimilarity: 90\n", "! only show sequence matches if their simlarity is at least this\n", "! value. This can be changed by the user within consed/assembly view/\n", "! by clicking on \"What to show/Sequence Matches\"\n", "! (OK)\n", "\n", "consed.tracesWindowInitialPixelWidth: 800\n", "! (OK)\n", "\n", "consed.assemblyViewWindowInitialPixelWidth: 800\n", "! (OK)\n", "\n", "consed.automaticallyScaleTraces: true\n", "! (OK)\n", "\n", "consed.automaticallyScaleTracesSamplePeakHeightFractionOfWindowHeight: 0.99\n", "! (OK)\n", "\n", "consed.automaticallyScaleTracesSamplePeakPercentile: 100\n", "! (OK)\n", "\n", "consed.verticalTraceMagnification: 30\n", "! (OK)\n", "\n", "consed.userDefinedKeys: 14 15\n", "! make a space-separated list of the decimal ASCII values of the keys\n", "! 14 means control-N, 15 means control-O\n", "! (OK)\n", "\n", "consed.programsForUserDefinedKeys: /bin/echo /bin/echo\n", "! a space-separated list of the full pathnames of the commands to run\n", "! This goes with consed.userDefinedKeys\n", "! (OK)\n", "\n", "consed.argumentsToPassToUserDefinedPrograms: argument_for_first_key argument_for_second_key\n", "! a space-separated list of the arguments to pass to the user-defined programs\n", "! This goes with consed.userDefinedKeys\n", "! (OK)\n", "\n", "consed.tagsToApplyWithUserDefinedKeys: none polymorphismConfirmed\n", "! a space-separate list of the tag types to apply when the user\n", "! presses a user-defined key. If a key is to have no associated tag,\n", "! then enter \"none\" for that key.\n", "! This goes with consed.userDefinedKeys\n", "! (OK)\n", "\n", "consed.snpGenomeUseInsertionPolymorphisms: true\n", "! used with consed -snpGenome\n", "! (OK)\n", "\n", "consed.listOfTagTypesToHide: matchElsewhereHighQual matchElsewhereLowQual\n", "! (OK)\n", "\n", "consed.listOfOptionalWordsToSaveInListOfReadNames: forward reverse ET BigDye customOligo SeqEx FS dyePrimer dyeTerminator doubleStranded singleStranded\n", "! (OK)\n", "\n", "consed.extendConsensusWithHighQuality: false\n", "! When using \"change consensus\" to extend the consensus, make the\n", "! read edited high quality. This will cause phrap, the next time\n", "! the project is assembled, to similarly extend the consensus. If\n", "! this is set to false, then do not change the quality of the read and \n", "! extend the consensus with the original read qualities. \n", "! (OK)\n", "\n", "consed.fastStartup: true\n", "! If you have used catPhdFiles.perl to create a huge file with all the\n", "! xxx.phd.1 files, and you have enough memory on your computer, then\n", "! you can startup up consed up to 7 times faster\n", "! (OK)\n", "\n", "consed.fastStartupFile: phd.ball\n", "! If you have used catPhdFiles.perl to create a huge file with all the\n", "! xxx.phd.1 files, and you have enough memory on your computer, then\n", "! you can startup up consed up to 7 times faster. This file gives\n", "! the name of the huge file.\n", "! (OK)\n", "\n", "consed.alwaysRunProgramToGetChromats: false\n", "! This allows consed to get chromats out of a database, or do some\n", "! other pre-processing of a chromat before reading it. If set to true,\n", "! consed does not look in ../chromat_dir at all for the chromat, but\n", "! rather runs the program listed in consed.programToRunToGetChromats\n", "! with argument name-of-read and then reads the chromat out of\n", "! consed.uncompressedChromatDirectory and then later deletes the\n", "! chromat from consed.uncompressedChromatDirectory\n", "! If set to false, it never does this. If set to \"last\", it does\n", "! this as a last resort.\n", "! (OK)\n", "\n", "consed.programToRunToGetChromats: /usr/local/bin/myFavoriteProgram\n", "! Set this to the program or script that you want to use to\n", "! get a chromat and put it into /tmp (or whatever you set\n", "! consed.uncompressedChromatDirectory to)\n", "! (OK)\n", "\n", "consed.programToRunToGetChromatsOf454Reads: $CONSED_HOME/bin/sff2scf\n", "! This will be run on 454 reads if the read is not found in\n", "! chromat_dir. If you don't want this to happen, you can make \n", "! this null.\n", "! (OK)\n", "\n", "consed.createFakeChromatsForSolexaReads: true\n", "! (OK)\n", "\n", "consed.autoFinishUseLongModelReadRatherThanShort: false\n", "! When calculating the distribution of quality values at high read \n", "! positions, should Autofinish assume that the reads that were this\n", "! long and longer are representative of finishing reads, or should it\n", "! assume that some finishing will not make it out this far in roughly\n", "! the same proportion as the existing reads.\n", "! (OK)\n", "\n", "\n", "consed.askAgainIfWantToQuitConsedIfThisManyReads: 500000\n", "! If you have to wait a long time for consed to come up, don't\n", "! quit out of consed by mistake.\n", "! (OK)\n", "\n", "consed.printWindowInstructions: Make sure that the window you want to print is unobscured. Then click \"Yes\" to dismiss this box. Then click on the window you want to print. You will hear a beep immediately, then another beep a little later. Then the copy of the window should come off the printer specified by your environment variable LPDEST.\n", "! (OK)\n", "\n", "consed.allowMultipleSearchForStringWindows: false\n", "! If this is false, and there is already a SearchForString Window up,\n", "! and the user clicks on SearchForString, it will be brought to the \n", "! front, rather than another one being created. \n", "! (OK)\n", "\n", "consed.autoPCRAmplifyFalseProductsOKIfLargerThanThis: 3000\n", "! If a pcr primer pair matches somewhere else and creates a product\n", "! larger than this, the pcr primer pair will still be acceptable\n", "! since the product will not easily form in the cycle time.\n", "! (OK)\n", "\n", "consed.autoPCRAmplifyMakePrimerOutOfFirstRegion: false\n", "! I don't expect people will use this. It allows you to amplify a\n", "! region using autoPCRAmplify not by allowing Consed to choose each\n", "! primer (the normal case) but rather by fixing the first primer to be\n", "! the first area bordering the region. I added this to allow\n", "! non-specific priming to the transplice leader.\n", "! (OK)\n", "\n", "consed.autoPCRAmplifyMaybeRejectPrimerIfThisCloseToDesiredProduct: 5000\n", "! ---> --->\n", "! false true match\n", "! In such a case, the primer pair will be rejected if the false is\n", "! within 5000 bases of true, even if false is a false match of the\n", "! other primer.\n", "!\n", "! <--- --->\n", "! false true match\n", "! In this case, the primer pair will not be eliminated.\n", "! (OK)\n", "\n", "\n", "consed.addNewReadsRecalculateConsensusQuality: false\n", "! When running consed by \n", "! consed -ace old_ace.ace -addReads fileOfPhdFiles.txt -newAceFilename new_ace.ace\n", "! consensus quality is recalculated\n", "! This also applies to add454Reads.perl and addSolexaReads.perl\n", "! (OK)\n", "\n", "consed.addNewReadsPutReadIntoItsOwnContig: ifUnaligned\n", "! choices are: \n", "! \"always\" (just put each read into its own contig)\n", "! \"ifUnaligned\" (put read into a contig if it aligns against the\n", "! consensus, otherwise put it into its own contig)\n", "! \"never\" (put read into a contig if it aligns against the consensus;\n", "! otherwise do not put it into the assembly) \n", "! (OK)\n", "\n", "consed.addNewReadsCheckThatCrossMatchRunCorrectly: true\n", "! addReads2Consed.perl changed in March 2008 to have -discrep_lists\n", "! instead of -alignments. Check that user is using the new \n", "! parameters\n", "! (OK) \n", "\n", "consed.assemblyViewNumberOfRowsOfTags: 4\n", "! (OK)\n", "\n", "consed.warnUserWhenTryingToEditAllReads: true\n", "! in the Aligned Reads Window, the user may change all reads at once\n", "! to a particular base at a particular position. This is dangerous\n", "! and the user is warned. This resource allows the user to suppress\n", "! this warning.\n", "! (OK)\n", "\n", "consed.maybeXKEYSYMDBPath: /usr/share/X11/XKeysymDB\n", "! Fixes a problem in X on some versions of linux giving pages of the \n", "! following errors:\n", "! Warning: translation table syntax error: Unknown keysym name: osfActivate\n", "! (OK)\n", "\n", "consed.maybeXKEYSYMDBPath2: /usr/X11R6/lib/X11/XKeysymDB\n", "! Fixes a problem in X on some versions of linux giving pages of the \n", "! following errors:\n", "! Warning: translation table syntax error: Unknown keysym name: osfActivate\n", "! (OK)\n", "\n", "\n", "consed.amountToMoveWithBigLeftAndRightArrows: 10\n", "! allows user to move on a read in the Aligned Reads Window\n", "! by more than 1 base at a time\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsMinDiscrepantReads: 2\n", "! ignores low quality reads\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsMaxDepthOfCoverage: 100000\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsIgnoreBasesBelowThisQuality: 20\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsJustListIndels: false\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsIgnoreOtherReadsStartingAtSameLocation: false\n", "! If there are, for example, 3 reads that all start at the same\n", "! location, use only the first and ignore the second and third\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus: false\n", "! Do not report this position if there is one of the bases in the consensus\n", "! listed in \n", "! consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus\n", "! (OK)\n", "\n", "consed.navigateByHighlyDiscrepantPositionsIgnoreIfTheseBasesInConsensus: xn\n", "! Do not report this position if there is one of these bases in the \n", "! consensus and if\n", "! consed.navigateByHighlyDiscrepantPositionsIgnoreIfListedBasesInConsensus:\n", "! is set to true\n", "! (OK)\n", "\n", "consed.phdBallDirectory: ../phdball_dir\n", "! phd balls are assumed to be in here. This is typically where consed\n", "! starts, but could be relative to that, such as ../phdball_dir \n", "! (OK)\n", "\n", "consed.newAceFileFOF: newAceFile.fof\n", "! if consed needs to write a new ace file, the name of that is written\n", "! to this file\n", "! (OK)\n", "\n", "consed.navigateByHighOrLowDepthCoalesceRegionsIfThisClose: 50\n", "! for navigate by high or low depth of coverage\n", "! (OK)\n", "\n", "consed.removeReadsDeleteNotJustPutInOwnContig: true\n", "! used for consed -removeReads and consed -removeContigs\n", "! (OK)\n", "\n", "consed.paired454LeftReadExtension: _left\n", "! (OK)\n", "\n", "consed.paired454RightReadExtension: _right\n", "! (OK)\n", "\n", "consed.snpGenome1MSnps: snp1M.txt\n", "! file for development of snpGenome\n", "! (OK)\n", "\n", "consed.diffChromosomesExcludeDeletions: false\n", "! for testing snpGenome moving deletions\n", "! (OK)\n", "\n", "consed.snpGenomeFilterByWeight: true\n", "! if true, only considers polymorphisms with soWeight == \"1\"\n", "! (OK)\n", "\n", "consed.wantReadsUpToThisFarFromSnps: 50\n", "! for phaster2PhdBall (phaster2Ace.perl ) to take reads, even if they don't overlap the\n", "! snp, that are this far away from the snp\n", "! (OK)\n", "\n", "consed.phaster2PhdBallSaveWhichMate: both\n", "! for phaster2PhdBall (phaster2Ace.perl) to determine whether\n", "! the function of just saving the reads that intersect the snp are \n", "! saved, or whether both mates of a read pair are saved if either one\n", "! intersects the snp location and has one of the desired alleles\n", "! alternative: unmapped which says that just the unmapped read is\n", "! saved\n", "! (OK)\n", "\n", "consed.phaster2PhdBallSaveInPhasterFormat: false\n", "! for phaster2PhdBall::maybeSaveBothReads to save the read in\n", "! phaster format rather than in phd format. This only applies\n", "! if consed.phaster2PhdBallSaveBothMates: is set to true\n", "! the phaster lines will be set to the file specified by\n", "! -phdBall on the command line\n", "! (OK )\n", "\n", "consed.phaster2PhdBallCalculateNewLocationsFile: false\n", "! for phaster2PhdBall. Calculates depth of coverage and\n", "! makes new locations that have depth of coverage \n", "\n", "\n", "consed.phdBall2FastaIgnoreLowQualityReads: false\n", "! for consed -phdBall2Fasta \n", "! if a read has mean quality below a threshold, do not\n", "! write it to the fasta file\n", "! (OK)\n", "\n", "consed.phdBall2FastaLowestAverageQuality: 25\n", "! for consed -phdBall2Fasta\n", "! if read has mean quality below this, ignore it\n", "! (OK)\n", "\n", "consed.nextPhredPipelineControlFile: control-file.txt\n", "! (OK)\n", "\n", "consed.nextPhredPipelineTiffPerlScript: bin/run_tiff2intens_1_tile.perl\n", "! (OK)\n", "\n", "consed.nextPhredPipelinePhasterPerlScript: bin/run_phaster_1_tile.perl\n", "! (OK)\n", "\n", "consed.nextPhredPipelineVersion: 100625\n", "! (OK)\n", "\n", "consed.nextPhredPipelineMainDirectory: /et/grc/vol3/np_testing/pipeline\n", "! (OK)\n", "\n", "\n", "\n", "!\n", "!\n", "!\n", "! parameters in the (NO) category\n", "!\n", "!\n", "consed.maxNumberOfReadsPerPhdBall: 1000000\n", "! This is important since cross_match slows down on fasta files of\n", "! over a few million reads \n", "! (NO)\n", "\n", "consed.userWantsToSaveToThisAceFile:\n", "! (NO)\n", "\n", "consed.autoFinishEmulate9_66Behavior: false\n", "! Picks univ primer reads and walks in the same phase. This results\n", "! in poor redundancy of universal primer reads, may pick custom primer\n", "! reads over universal primer reads, but may pick fewer\n", "! reads overall.\n", "! (NO)\n", "\n", "consed.primersPCRPrimersGroupedIntoWindowOfThisManyBases: 200\n", "! to speed up PCR primer picking and to reduce the number of \n", "! PCR primer pairs, group primers into windows of this size\n", "! and then just compare window against window\n", "! (NO)\n", "\n", "consed.primersLookForThisManyPCRPrimerPairsPerPairOfGroups: 2\n", "! to speed up PCR primer picking and to reduce the number of PCr\n", "! primer pairs, group primers into windows and then just accept\n", "! this many primer pairs from a pair of groups\n", "! (NO)\n", "\n", "consed.autoFinishStandardDeviationsFromMeanFromGapToLookForTemplatesForSuggestingEachMissingReadOfReadPairs: -1.0\n", "! Only applies when consed.autoFinishNearGapsSuggestEachMissingReadOfReadPairs:\n", "! is set to true. If m is the mean insert size and d is the standard\n", "! deviation and this parameter is p, then consider all templates\n", "! within a distance m + p*d from the gap.\n", "! (NO)\n", "\n", "consed.autoFinishCheckThatReadsFromTheSameTemplateAreConsistent: true\n", "! I strongly advise keeping this true. If you change it to false, you\n", "! are on your own. If the forward and reverse universal primer reads\n", "! look like this: <--- ---->, how is autofinish going\n", "! to even know where the template is, huh? Leave it true!\n", "! (NO)\n", "\n", "consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloseTogether: true\n", "! at higher redundancy, autofinish may pick custom primer reactions\n", "! that are only a few bases apart on the same strand. This parameter,\n", "! along with\n", "! consed.autoFinishDoNotAllowSubcloneCustomPrimerReadsCloserThanThisManyBases,\n", "! says how far apart they can be\n", "! (NO)\n", "\n", "consed.autoFinishDoNotAllowWholeCloneCustomPrimerReadsCloseTogether: true\n", "! Even at redundancy 1, Autofinish may pick whole clone reads just\n", "! a few bases apart. This prevents it.\n", "! (NO)\n", "\n", "consed.autoFinishMinilibrariesPreferTemplateIfSizeThisManyStdDevsFromMean: 2.0\n", "! If a template is more than this many standard deviations from the\n", "! mean, try to avoid using it, unless there is nothing else.\n", "! Rationale: there is something wrong with this template--an insertion\n", "! or deletion.\n", "! (NO)\n", "\n", "consed.autoFinishMinNumberOfForwardReversePairsInLibraryToCalculateAverageInsertSize: 5\n", "! If there are at least this many fwd/rev pairs in a library, then \n", "! the mean and standard deviation are used for sizing other templates in\n", "! the same library. If there are fewer than this, then the default size \n", "! specified in the librariesInfo.txt file is used.\n", "! (NO)\n", "\n", "consed.autoFinishIfEnoughFwdRevPairsUseThisManyStdDevBelowMeanForInsertSize: 0.2\n", "! If you are interested in walking on a template that does not have a\n", "! forward/reverse pair, then the precise insert size is uncertain. If\n", "! this template comes from a library that has lots of templates with\n", "! forward/reverse pairs, then the mean and standard deviation of the\n", "! insert sizes from this library is known. For the template in\n", "! question, we could just use the mean of this library (this parameter =\n", "! 0.0), but we could be conservative and assume the insert size is\n", "! somewhat less. This parameter tells how much less.\n", "! (NO)\n", "\n", "consed.autoFinishNewCustomPrimerReadThisFarFromOldCustomPrimerRead: 50\n", "! this tells autofinish when it wants to make a new custom primer\n", "! read, how far this read must be from any previous custom primer\n", "! reads on the same strand\n", "! (NO)\n", "\n", "consed.autoFinishMinNumberOfSingleSubcloneBasesFixedByAnExp: 1\n", "! if an experiment will only fix less than this number of single\n", "! subclone bases, don't do it even if the total number of single\n", "! subclone bases in the contig is too high\n", "! (NO)\n", "\n", "consed.autoFinishNumberOfBasesBetweenContigsAssumed: 1000\n", "! gap size--each base in the gap counts as 1 error so autofinish tries\n", "! to extend into gaps\n", "! (NO)\n", "\n", "consed.autoFinishPotentialHighQualityPartOfReadStart: 80\n", "! nReadUnpaddedConsPosStart + nAutoFinishPotentialHighQualityPartOfReadStart_\n", "! == nReadUnpaddedConsPosStartOfPotentialHighQuality\n", "! this is used to evaluate the quality of templates\n", "! this no longer has much effect on the reads autofinish chooses\n", "! (NO)\n", "\n", "consed.autoFinishPotentialHighQualityPartOfReadEnd: 300\n", "! nReadUnpaddedConsPosStart + nAutoFinishPotentialHighQualityPartOfReadEnd_\n", "! == nReadUnpaddedConsPosEndOfPotentialHighQuality\n", "! this is used to evaluate the quality of templates\n", "! this no longer has much effect on the reads autofinish chooses\n", "! (NO)\n", "\n", "consed.autoFinishPrintCustomNavigationFileForChosenReads: true\n", "! If this is true, then autofinish will print a file of the chosen reads\n", "! in the format for consed to navigate (prev and next) to each\n", "! location of the proposed new reads\n", "! (NO)\n", "\n", "consed.autoFinishReversesForFlankingGapsTemplateMustProtrudeFromContigThisMuch: 100\n", "! Normal case:\n", "! --------------------------- (consensus)\n", "! ----------- template1\n", "! ----------- template2\n", "! ----------- template3\n", "! Then you probably would want to use template3 since a reverse is\n", "! most likely to go in the other contig rather than go into gap.\n", "! But suppose that template2 and template3 don't exist. Would you\n", "! want to use template1? This parameter tells Autofinish whether you\n", "! would want to use it, or pick no reverse at all.\n", "! (NO)\n", "\n", "consed.autoFinishTagOligosWhenDoExperiments: true\n", "! when autofinish is run with -doExperiments, tags the oligos\n", "! it chooses\n", "! (NO)\n", "\n", "consed.countPads: false\n", "! (NO)\n", "\n", "consed.debugging: 0\n", "! for consed development use\n", "! (NO)\n", "\n", "consed.debugging2: 0\n", "! for consed development use\n", "! (NO)\n", "\n", "consed.debugging3: 0\n", "! for consed development use\n", "! (NO)\n", "\n", "consed.debuggingString: joseph\n", "! for consed development use\n", "! (NO)\n", "\n", "consed.ignoreHighQualityDiscrepanciesThisManyBasesFromEndOfAlignedRegion: 5\n", "consed.ignoreUnalignedHighQualitySegmentsShorterThanThis: 20\n", "! (NO)\n", "\n", "consed.primersLookThisFarForForwardVectorInsertJunction: 125\n", "! don't change this--if no X's this far from beginning of read, then\n", "! assume that you are in insert\n", "! (NO)\n", "\n", "consed.primersDNAConcentrationNanomolar: 50.0\n", "! used for melting temperature--don't change this!\n", "! (NO)\n", "\n", "consed.primersMaxMatchElsewhereScore: 17\n", "! used for testing false-annealing to template and to vector\n", "! (NO)\n", "\n", "consed.primersMaxMatchElsewhereScoreForPCR: 21\n", "! used for testing false-annealing to template and to vector\n", "! when used with PCR\n", "! (NO)\n", "\n", "consed.primersMaxSelfMatchScore: 6\n", "! cutoff for self-annealing of a primer\n", "! (NO)\n", "\n", "consed.primersMaxPrimerDimerScoreForPCR: 14\n", "! careful changing this\n", "! (NO)\n", "\n", "consed.primersMinQuality: 30\n", "! you must be sure of the sequence of a primer or it won't anneal to\n", "! where you want\n", "! (NO)\n", "\n", "consed.primersPrintInfoOnRejectedTemplates: true\n", "! whether to print which templates were rejected and why (this output\n", "! can be large )\n", "! (NO)\n", "\n", "consed.primersSaltConcentrationMillimolar: 50.0\n", "! used for melting temperature--don't change this!\n", "! (NO)\n", "\n", "consed.primersScreenForVector: true\n", "! whether or not to screen primers for annealing to vector\n", "! (NO)\n", "\n", "consed.primersToleranceForDifferentBeginningLocationOfUniversalPrimerReads: 100\n", "! different forward reads or different reverse reads \n", "! can differ by up to this amount in the starting location\n", "! If they differ by more, then there is something wrong\n", "! with the template (it is mislabeled?) so don't use it again for\n", "! walking\n", "! (NO)\n", "\n", "consed.primersTooManyVectorBasesInWalkingRead: 10\n", "! if there are this many x's, then don't walk again on this template\n", "! (NO)\n", "\n", "consed.qualityThresholdForLowConsensusQuality: 25\n", "! highest low quality. A base at this quality is considered low\n", "! quality. A base higher than this is considered high quality.\n", "! (NO)\n", "\n", "consed.tagColorPerCentOfBase: 50\n", "! (NO)\n", "\n", "consed.uncompressedChromatDirectory: /tmp\n", "! (NO)\n", "\n", "consed.454sff2scfDirectory: /tmp\n", "! when a user asks to see a 454 trace, and sff2scf runs, the\n", "! scf file will be put here. This is hard-coded in sff2scf.c\n", "! (NO)\n", "\n", "consed.whenMakingFakeReadToJoinContigsAddThisManyBasesOnEitherSideOfAlignedRegion: 200\n", "! (NO)\n", "\n", "consed.writeThisAceFormat: 2\n", "! (NO)\n", "\n", "consed.dumpCoreIfBoundsError: false\n", "! (NO)\n", "\n", "\n", "consed.autoFinishMinSmithWatermanScoreOfARun: 20\n", "! (NO) \n", "\n", "consed.autoFinishDoNotComparePCRPrimersMoreThanThisManyTimes: 1.0e+9\n", "! When autofinish tries to find a compatible set of pcr primers, it\n", "! can take billions of tries. This limits the number of tries so that,\n", "! if autofinish can't find it in this number of tries, it gives up\n", "! rather than running for days, weeks, years!\n", "! (NO)\n", "\n", "consed.restrictionDigestMaximumBasesToCompareToVector: 200\n", "! (NO)\n", "\n", "consed.restrictionDigestZoomFactor: 2.0\n", "! Amount to zoom in or out in the gel window of the restriction digest\n", "! (NO)\n", "\n", "consed.restrictionDigestZoomFactorForNavigate: 10.0\n", "! When looking at restriction gel and navigating to first problem\n", "! location, this is the amount to zoom in.\n", "! (NO)\n", "\n", "consed.restrictionDigestToleranceInPositionUnits: 20\n", "! (NO)\n", "\n", "consed.autoPCRAmplifyTooManySeriousFalseMatches: 100\n", "! If a pcr primer pair has a significant false match to this many\n", "! other places in the assembly, do not consider for possible pcr\n", "! primer pairs. This is just for the purpose of speeding up picking\n", "! of primer pairs--the higher the number, the faster the searching,\n", "! but the more likely a primer pair will be selected that will\n", "! create multiple products.\n", "! (NO)\n", "\n", "consed.assemblyViewZoomFactor: 1.5\n", "! amount to zoom in or out\n", "! (NO)\n", "\n", "consed.assemblyViewFilterInconsistentFwdRevPairsIfThisClose: 2000\n", "! If forward/reverse pairs start this close together and end this\n", "! close together, they confirm each other.\n", "! (NO)\n", "\n", "consed.assemblyViewGridCellWidthInPixels: 4.0\n", "! for keeping track where objects are on screen. If you make it\n", "! larger, you get better drawing performance, but lower resolution\n", "! of which objects the cursor is pointing at\n", "! (NO)\n", "\n", "consed.assemblyViewCursorSensitivityInPixels: 4\n", "! square about cursor that will detect objects\n", "! (NO)\n", "\n", "consed.assemblyViewReadDepthQuality: 20\n", "! (NO)\n", "\n", "consed.showAllTracesMaxNumberOfTracesToShowAtOnce: 100\n", "! (NO)\n", "\n", "consed.allowFwdRevPairScaffoldsToBeMergedIfThisManyBasesIntersectionOrLess: 1000\n", "! (NO)\n", "\n", "consed.justForPrimateProject: false\n", "! (NO)\n", "\n", "consed.solexaFilesAreAssumedToBeHere: ../solexa_dir\n", "! any solexa files (or links) are assumed to be in this directory. \n", "! If you change this, it can have effects in 3 places: 1) add new\n", "! reads list of solexa files 2) add new reads where it looks for these\n", "! files and 3) subsequent runs of consed it will prepend this to the\n", "! path it finds in the ace file under PHD_DIR: on the DS line. There\n", "! may be other implications as well.\n", "! (NO)\n", "\n", "consed.solexaAlignmentFilesPerInsertingPadsCycle: 50\n", "! (NO)\n", "\n", "consed.solexaAlignmentsPerAlignmentFile: 10000\n", "! (NO)\n", "\n", "consed.solexaFastqFilesArePhredQualityNotSolexaQuality: true\n", "! (NO)\n", "\n", "consed.solexa64FastqOrSanger33Fastq: auto\n", "! valid values are: auto (it figures it out itself),\n", "! solexa64 (+64), and sanger33 (+33)\n", "! If consed is being fooled, you can set these to force\n", "! consed to override what the file appears to be.\n", "! (NO)\n", "\n", "consed.maximumReadsInReadList: 200000\n", "! even if there are millions of reads, don't display them all or\n", "! it will eat up memory and time\n", "! (NO)\n", "\n", "\n", "consed.maxLengthOfReadsInapLocatedFragment2: 10000\n", "! (NO)\n", "\n", "consed.maximumStartupErrorsToReport: 50\n", "! (NO)\n", "\n", "consed.454LinkerAlignmentMatchScore: 1\n", "! (NO)\n", "\n", "consed.454LinkerAlignmentMismatchScore: 3\n", "! (NO)\n", "\n", "consed.454LinkerAlignmentIndelScore: 2\n", "! (NO)\n", "\n", "consed.filter454ReadsDeleteCrossMatchOutput: true\n", "! This should be changed to false only for troubleshooting. \n", "! Otherwise unused files will accumulate on your disk.\n", "! (NO)\n", "\n", "\n", "! These additional consensus bases are added for the miniassembly\n", "! of the reads on the end of the contig. \n", "! (NO)\n", "\n", "\n",