Reverse Complement Human Genome Reference
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7.0 years ago
L. A. Liggett ▴ 120

I am using hg19.fa for my alignments and for a particular control I was thinking of running I would like to align to the negative strand of the reference genome. I took the reverse complement of hg19 and then index with bwa index but it will not index. Is there a way to properly do this?

sequencing • 1.7k views
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7.0 years ago
GenoMax 143k

Aligners always look at both strands when aligning.

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Yes, perhaps you can do that after mapping by scripts.

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