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Question: do you need to reverse complement read 2 in aligning paired end reads?
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gravatar for epigene
4.1 years ago by
epigene • 450
United States
epigene • 450 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?? 

http://seqanswers.com/forums/showthread.php?t=18158

 
alignment paired-end • 1.5k views
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modified 4.1 years ago by Pierre Lindenbaum ♦ 122k • written 4.1 years ago by epigene • 450
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gravatar for Pierre Lindenbaum
4.1 years ago by
Pierre Lindenbaum ♦ 122k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 122k 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 COMMENT • link written 4.1 years ago by Pierre Lindenbaum ♦ 122k

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

 

ADD REPLY • link written 4.1 years ago by epigene • 450
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