Hi,
I have a list of contig names. How can I filter those out from a FASTQ file to work on the left file?
I have a list of contig names. How can I filter those out from a FASTQ file to work on the left file?
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Using BBMap:
filterbyname.sh in=contigs.fa out=filtered.fa names=names.txt
The names can either be a file containing one name per line, or a comma-delimited list of names. filterbyname works on fasta or fastq; I assume by fastq you actually meant fasta, but either is fine. If you output name ends with .fq or .fastq the output will be a fastq file; if it ends with .fa or .fasta it will be a fasta file. -
Here's one of my Python scripts intended for use within Galaxy (or at the command line) that ought to do this:
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