NAME

createAnchorTagsForAce.pl

SYNOPSIS

  createAnchorTagsForAce.pl [options] <454Scaffolds.txt> <gapDirsFile> <outputAnchorFile>
    
  Options:
  -a <file>          ace file (optional; if specified then ace file will be tagged)
  -log <file>        log file (optional; default is createAnchorTagsForAce.pl.log)
  -warn <file>       warnings log file (optional; default is defined in gapRes.config)
  -d                 Debug mode. Prints additional information in output file (optional)
  -h                 Detailed help message                                    (optional)

DESCRIPTION

This software component is part of the Gap Resolution sub system that is responsible for creating an output of tags that specify the coordinates of the anchors in the acefile. The anchor tags are then added to the specified ace file.

Unless otherwise noted, anchor here refers to the anchor sequence obtained from the left and right contigs of the gap prior to reassembly. This is done upstream using idContigRepeats.pl.

The ouput of idRepeatBoundaries.pl is used, in conjunction with the size and orientation of each contig within its scaffold, as specified in the 454Scaffolds.txt file, to calculate the position of each anchor. This information is then used to create a consed formatted output file of tags.

A default config file named gapRes.config residing in <installPath>/config is used to specify the following parameters:

(configurable)

  createAnchorTagsForAce.allowTransferOfTags
    Allow transfer of ace tags using transferConsensusTags (provided in 
    Phred/Phrap/Consed package).  Set to 1 for transferability, zero for 
    non-transferability.
  createAnchorTagsForAce.tagType
    Name of tag type when adding tag to ace file.

(system configuration)

  createGapResProject.assemInfoDirName
  idContigRepeats.scaffFileName
  idContigRepeats.boundaryFileExtension
  idRepeatBoundary.uniqueAnchorLength
  script.aceTagger

VERSION

$Revision: 1.11 $

$Date: 2010-01-13 00:26:00 $

AUTHOR(S)

Kurt M. LaButti

HISTORY