Rationale:
Magicblast creates a list of reads from a read file that match a
user-created BLAST database. The list can then be used to
eliminate reads from the original read file, or to extract hits
from the read file. Magicblast can create two types of files:
files containing reads that match the database, files containing
reads that do NOT match the database, or both files. This can be
useful, for example, if you were sequencing a eukaryotic genome
and wanted to eliminate contaminating reads from prokaryotic
symbionts whose DNA co-purified with the host.
Where:
Run magicblast in the same folder as your read files. Before
running magicblast, select read files from blreads. Groups of
files can be processed as paried end files using File -->
guesspairs.
Input:
Input read
files may be gzipped or uncompressed. Both fastq and fasta files
are supported. There MUST be a file extension to indicate which
type of file is being read. For example, reads.fq, reads.fastq,
reads.fq.gz or reads.fastq.gz are all acceptable names for a fastq
file. reads.gz will be flagged as an unknown type of file.
Database - This may be either a BLAST
database created using makeblastdb, or a fasta file. Searching a
BLAST database is much faster than searching a fasta file. BLAST
databases consist of several files eg. Zmays-mito.ndb,
Zmays-mito.nhr, Zmays-mito.nin etc. Selecting any of the files for
a database will select that database.
Magicblast Parameters:
See magicblast manual page.
SeqKit grep
Parameters:
Extract reads to new file(s)?
Optionally, you can ask magicblast to create files containing
subsets of reads:
- None
- write a matching reads file - Reads that match the
database will be written to a file combining the readfile name
with the name of the database, and a + to indicate matching. eg.
If the readfile name was M400.fastq.gz, and the database was
Zmays-mito, the file of matches would be
M400.Zmays-mito+.fastq.gz
- write a mismatching reads file - Reads that do NOT
match the databse will be written using a - to inidcate
mismatching eg. M400.Zmays-mito-.fastq.gz
- both - both + and - files are written
Output:
Name for output directory - This defaults to the
current directory. That makes sense, because the output from
magicblast will be used for extracting reads from files in this
directory.
The list of files in the current directory will be refreshed in
blreads.