liftOver narrowPeak file
1 answer
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".
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arturtjaro •
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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.
Just curious have you figured this out?