Converting PE to SE

Question

[Picasa]

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) ?

[Carlo Yague]

Why don't you map the PE and SE reads separately, then merge the resulting two bam files ?

[GenoMax]

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 append

[Picasa]

Thanks for your answer, but I need to be sure that I understand how R2 is :

the reverse complement or only reverse ?

[GenoMax]

No change. read2.fq.gz is used as is.