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Old 04-02-2019, 04:54 AM   #669
GenoMax
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,015
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@seqmore: I don't see you actually providing the sequence index you made in step 1 to your bbmap.sh command.

It would be included using "path=dir_with_index" in

Code:
$bbmap.sh maxindel=200k intronlen=20 ambig=all xstag=unstranded xmtag=t in=a.fq out=a.bbmap.sam outu=a.unbbmap.fq bs=script.sh
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