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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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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...
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