Does BWA align the same read in forward and its reverse complement?

Question

[thenameisizaak]

Hi All, Given each read, will BWA try to align that read to the reference genome in both forward and reverse orientation?

As my understanding, hg 19 for example is represents one sense strand of the human genome. Therefore, if a read is from the opposite sense, it will not align, thus, if BWA cannot align a read, does it then convert to rev. comp and then try aligning again?

Best, Izaak

Answer 1

[Devon Ryan]

Yes, every aligner I'm familiar with will attempt to align reads in both orientations (unless they're told not to).