liftOver narrowPeak file
1
0
Entering edit mode
4.7 years ago
rbronste ▴ 400

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

liftOver Assembly • 1.5k views
ADD COMMENT
1
Entering edit mode

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
1
Entering edit mode
8 months ago
arturtjaro ▴ 10

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".

ADD COMMENT

Login before adding your answer.

Traffic: 1029 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6