Question: Converting narrowPeak to bed
2
gravatar for Spacebio
2.5 years ago by
Spacebio180
Spacebio180 wrote:

Hi all,

I am trying to convert a regular narrowPeak file into a BED file for use with diffBind... any ideas?

Thanks.

narrowpeak bed • 3.8k views
ADD COMMENTlink modified 2.5 years ago by Rory Stark600 • written 2.5 years ago by Spacebio180
2
gravatar for h.mon
2.5 years ago by
h.mon29k
Brazil
h.mon29k wrote:

Do you really need to convert? narrowPeak already is in bed 6+4 format, see here, here and here.

edit: in case DiffBind if very strict, use this solution:

cut -f 1-6 macs_output.narrowPeak > macs_output.bed
ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by h.mon29k

I tried but it is not working, any other suggestion? Thanks for your help!

ADD REPLYlink written 2.5 years ago by Spacebio180

Yes, describe how it is not working. What have you been trying? Errors you got?

ADD REPLYlink written 2.5 years ago by h.mon29k

the sample sheet is the more likely problem....the narrowPeak file doesnt need any editing.

ADD REPLYlink written 2.5 years ago by YaGalbi1.5k

But then how can I obtain the count matrix? For that reason I wanted to convert the narrowPeak to bed because i already established the pipeline in that way. Any suggestion is very appreciated.

ADD REPLYlink written 2.5 years ago by Spacebio180
2
gravatar for Rory Stark
2.5 years ago by
Rory Stark600
University of Cambridge, Cancer Research UK - Cambridge Institute
Rory Stark600 wrote:

DiffBind supports narrowPeak format directly, Just specify "narrow" as the value for PeakCaller in your samplesheet.

-Rory

ADD COMMENTlink written 2.5 years ago by Rory Stark600

I have the narrowPeak files, I want to extract the counts to use the matrix with DESeq or EdgeR. That is why I was trying to convert the narrowPeak files into bed files. Any suggestion?

ADD REPLYlink modified 2.5 years ago • written 2.5 years ago by Spacebio180
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