do you need to reverse complement read 2 in aligning paired end reads?
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?
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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".
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Pierre Lindenbaum
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