Question: do you need to reverse complement read 2 in aligning paired end reads?
gravatar for epigene
4.7 years ago by
United States
epigene490 wrote:

I thought you just give the read1 and read2 files to a aligner without reverse complementing read2. However, someone in this post suggested to reverse complement read2 before alignment? Is that true at all??


alignment paired-end • 1.6k views
ADD COMMENTlink modified 4.7 years ago by Pierre Lindenbaum127k • written 4.7 years ago by epigene490
gravatar for Pierre Lindenbaum
4.7 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum127k wrote:

An important part of the  seqanswers question is :

"If I wanted to combine these into one long read"

to you really want to merge the reads ?

For a classical paired-end mapping with bwa/bowtie, you don't have to reverse-complement the reads. Check the SAM flags at the end: most of the reads should be flagged "properly-paired".

ADD COMMENTlink written 4.7 years ago by Pierre Lindenbaum127k

ok, cool, that's what i thought. thanks


ADD REPLYlink written 4.7 years ago by epigene490
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