4 answers
I also wrote a program for this purpose, distributed with BBMap. Usage:
filterbyname.sh in=reads.fq out=filtered.fq names=names.txt include=t
The include flag will toggle between including or excluding the names in names.txt (which can, alternately, be another fastq or fasta file). This also supports paired input/output, and names being substrings or superstrings of read IDs.
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Brian Bushnell
I prefer writing my own little snippets. However, it's possible using biopieces. This reply is from seqanswers (by maasha), pasted here for convenience.
First you need a file with the FASTQ sequence names you are interested in - or IDs if you like - one per line. And then:
read_fastq -i in.fastq | grab -E ids.txt | write_fastq -xo out.fastqCheck out grab for details.
It is simpler to go back to the original .bam, and just pull out the .bam entries that are unmapped. samtools view -f4 should do it. Then, you can use something like Picard's SamToFastq to go back to fastq format, if you need to. (Some software, like velvet, is fine with using .bam as input)
I've found a quick solution with cdbfasta and cdbyank tools.
First you have to index your fastq with cdbfasta, then you can search for the IDs in fastq with cdbyank. For more info http://sourceforge.net/projects/cdbfasta/
Thank you,
Luke
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I have a post here which addresses part of this question