Converting narrowPeak to bed
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4.2 years ago
Spacebio ▴ 200

Hi all,

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

Thanks.

narrowPeak BED • 7.4k views
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I know this is an old ticket however I am not able to create a DBA object with a narrowPeak file as it complains about the first line in the narrow peak file not having 10 columns which is true because it has a header like this:

track type=narrowPeak visibility=3 db=hg19 name="nPk" description="ENCODE narrowPeak Example"
browser position chr1:9356000-9365000
chr1    9356548 9356648 .       0       .       182     5.0945  -1  50
chr1    9358722 9358822 .       0       .       91      4.6052  -1  40
chr1    9361082 9361182 .       0       .       182     9.2103  -1  75

Only after removing the header, I was able to load it. Is this okay or something is off about my peak calling? Here's the code snippet

allsamples <- read.csv('meta/allsamples.csv')
gpparestTestbeta <- dba(sampleSheet=allsamples)
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4.2 years ago
Rory Stark ★ 1.3k

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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4.2 years ago
h.mon 33k

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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