I know, this question is everywhere. But I have yet to see somebody use the same samotols command as myself, and I wanted to double-check.
samtools view -S -f 4 aligned.sam > unmapped.sam
Try it. If reads with a * in chromosome field are gone then you are all set.
Just to clarify, the * in the chromosome signifies unmapped reads? So, in the above command, since I am extracting unmapped reads into a separate file, that file should have mostly reads with * in the chr field.
Your way is fine. The -S is optional; the default behavior of samtools view is to output as sam, not bam.
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