Converting narrowPeak to bed

Question

[Spacebio]

Hi all,

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

Thanks.

[deepak.tyagi2326]

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)

[Ram]

Please do not add an answer unless you're answering the top level question. You have a related question, which is best posted as either a comment on the top level question or as a new question referencing the existing question.

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Answer 1

[h.mon]

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

[Spacebio]

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

[h.mon]

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

[BioinfGuru]

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

[Spacebio]

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.

[Melih]

It worked for me, thank you very much

Answer 2

[Rory Stark]

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

-Rory

[Spacebio]

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?