Hi all, Sorry if this already has a clever answer, but I failed to figure it out. I am trying to collect and merge all the unmapped reads from many bam files. I can run samtools merge -R 'contig' but how do you run it for unmapped '*' I tried quotes escaping but no luck. I know samtools view and flags can do it but I have many files generated in a pipeline and I like to extract all the unmapped reads in a separate file for other analysis. Samtools view does not take multiple inputs so merge will work the best. Any thoughts anybody?
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