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Old 06-07-2017, 09:44 AM   #5
Brian Bushnell
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Location: Walnut Creek, CA

Join Date: Jan 2014
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Yep - you can use "covstats=covstats.txt covhist=covhist.txt" to print the coverage information of the whole genome as well as on a per-scaffold basis, and also give a distribution of base coverage over the genome. For more information see the "Coverage output parameters" section of bbmap.sh. Once the reads are mapped, using the sam or bam file, you can do the same thing with pileup.sh.
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