do you need to reverse complement read 2 in aligning paired end reads?

Question

[epigene]

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

Answer 1

[Pierre Lindenbaum]

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".

[epigene]

OK, cool, that's what I thought. Thanks