Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Tutorials
Tools
Jobs
Forum
Planet
All »
Home
Log In
Question: do you need to reverse complement read 2 in aligning paired end reads?
0
gravatar for epigene
4.7 years ago by
epigene • 490
United States
epigene • 490 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 • 1.6k views
ADD COMMENT • link •
modified 4.7 years ago by Pierre Lindenbaum ♦ 127k • written 4.7 years ago by epigene • 490
2
gravatar for Pierre Lindenbaum
4.7 years ago by
Pierre Lindenbaum ♦ 127k
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum ♦ 127k 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 4.7 years ago by Pierre Lindenbaum ♦ 127k

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

 

ADD REPLY • link written 4.7 years ago by epigene • 490
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1731 users visited in the last hour