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Converting narrowPeak to bed
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2.4 years ago
Spacebio • 180

Hi all,

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

Thanks.

narrowPeak BED • 2.5k views
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17 months ago
h.mon 25k
Brazil

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

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

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

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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.

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16 months ago
Rory Stark • 510
University of Cambridge, Cancer Researc…

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

-Rory

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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?

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