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Bed to BedGraph

I am a bit confused.

Would you please guide me. I want to use DaPars. It need a BedGraph file as input.

I have searched and understand it is possible to covert bed to bedgraph! But how the coverage could be defined then? In DaPars the coverage in needed to find if there is any alternative polyadenylation.

rna-seq dapars bedgraph bed
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updated by Ram Ram • written by Ati • Ati

Two easy ways to make Bedgraph from BED input with common Unix tools are with cut

$ cut -f1-3,5 foo.bed > foo.bedgraph

And with awk:

$ awk '{ print $1"\t"$2"\t"$3"\t"$5 }' foo.bed > foo.bedgraph
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updated by Ram Ram • written by Alex Reynolds Alex Reynolds

Thanks a lot, would you please let me know how to convert wig to BedGraph?

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written by Ati • Ati

You can use wig2bed:

$ wig2bed < foo.wig | cut -f1-3,5 > foo.bedgraph
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written by Alex Reynolds Alex Reynolds

Thanks, I got this error wig2bed: line 156: convert2bed: command not found

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updated by Ram Ram • written by Ati • Ati

Install all the binaries into one place available from your path, like /usr/local/bin etc.

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written by Alex Reynolds Alex Reynolds

Of course I did it but I still face this error

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updated by Ram Ram • written by Ati • Ati

1 answer

How to generate BedGraph from BedTools Coverage? might be a good place to start looking.

Essentially you can use bedtools genome coverage tool to find coverage in your bed file and then output the format as a bedGraph using the -bg parameter.

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updated by Ram Ram • written by dally dally

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