I obtained a list of unmapped reads IDs from my BAM file and I want to remap only the unmapped reads with other parameters.
How can I extract the subset of unmapped reads from my original fastq file?
Thank you in advance,
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.
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)