do you need to reverse complement read 2 in aligning paired end reads?
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7.6 years ago
epigene ▴ 570

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

paired-end alignment • 2.5k views
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7.6 years ago

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

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