Question

liftOver narrowPeak file

0

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7.2 years ago

rbronste ▴ 420

I am wondering how you can use liftOver to convert mm10 narrowPeak files back to mm9? Thanks.

liftOver Assembly • 2.9k views

ADD COMMENT • link updated 2.5 years ago by kai_bio ▴ 50 • written 7.2 years ago by rbronste ▴ 420

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Just curious if you've ever figured this out. I'm wondering the same for GRCh38-mapped narrowPeak files to hg19. I suspect getting rid of the offending columns is not advisable.

ADD REPLY • link 6.8 years ago by phosphodiester_bond ▴ 40

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Just curious have you figured this out?

ADD REPLY • link 2.5 years ago by kai_bio ▴ 50

score 1 · Answer 1 · 2021-01-26

I just stumbled upon this problem, and it turns out the solution is very easy:

liftOver \
-bedPlus=6 \
sample.narrowPeak.gz \
mm10Tomm9.over.chain.gz \
sample.lifted.narrowPeak \
sample.unmapped.narrowPeak

The important line here is -bedPlus=6. This will treat only the first 6 columns in your input file as a BED file. The rest of the columns will just be "carried along for the ride".