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There used to be an option to output all unmapped reads to a separate file, but it appears to no longer be an option. Are the unmapped reads printed to the sam file? If so, I assume there is an easy way to extract those data...if I was more proficient at scripting?
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I don't know what if anything in bfast has changed, however...
If a SAM file contains both mapped and unmapped reads, you can filter this using the FLAG field. -
As maubp mentions, if you used -a3 during postprocess (recommended), you can run:
$ samtools view -f4 my.bam > unmapped_reads.sam-drdComment
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