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Old 04-26-2014, 09:22 AM   #32
Thias
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Location: Münster, Germany

Join Date: Mar 2013
Posts: 42
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Quote:
Originally Posted by Brian Bushnell View Post
bbmap.sh in1=read1.fq.gz in2=read2.fq.gz ref=zv9.fa out=mapped.sam maxindel=200000
@ Brian: Is maxindel the only bbmap parameter you recommend to change for mapping reads for subsequent Cufflinks analysis?

Because I interpetreted the Cufflinks Doc in a way, that it will use the xmtag to lower the read weight by the amount of sites it maps to and therefore decided to set ambig=all.

I therefore chose to set for my RNAseq:

Code:
maxindel=200000 intronlen=10 ambig=all xstag=unstranded xmtag=T
Was I misled?
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