Converting PE to SE
Hello,
I have RNAseq paired end in fr-firststrand (as described here http://chipster.csc.fi/manual/library-type-summary.html).
I have also RNA reads in single end (reverse orientation).
I need to perform a mapping but since it cannot handle a mix of PE and SE, I have to transform my PE into SE (and make it to the same orientation).
I have a doubt, is it correct that I just have to reverse complement my R2 (my PE) ?
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Why don't you map the PE and SE reads separately, then merge the resulting two bam files ?
BBMap can take in PE and SE data in at the same time.
bbwrap.sh in1=read1.fq.gz,singletons.fq.gz in2=read2.fq.gz,null out=mapped.sam appendThanks for your answer, but I need to be sure that I understand how R2 is :
the reverse complement or only reverse ?
No change.
read2.fq.gzis used as is.