I am trying to convert a regular narrowPeak file into a BED file for use with diffBind... any ideas?
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
I tried but it is not working, any other suggestion? Thanks for your help!
Yes, describe how it is not working. What have you been trying? Errors you got?
the sample sheet is the more likely problem....the narrowPeak file doesnt need any editing.
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.
DiffBind supports narrowPeak format directly, Just specify "narrow" as the value for PeakCaller in your samplesheet.
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?