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Converting Bed files to bedGraph

I downloaded a bed file from UCSC web genome browser, and now I would like to convert it to .bdg or bedGraph format. I've been looking around for a while but nothing seems to work. I have bedtools downloaded if that helps.

Thank you

chip-seq software-error
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updated by Ram Ram • written by dally dally

Your response is at first glance snarky, but the link is absolutely appropriate, and posted with experience of having gathered 75,000 internet points. Good response.

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written by Joseph Pearson Joseph Pearson

1 answer

I would recommend carefully studying the bedgraph format specification:

http://genome.ucsc.edu/goldenpath/help/bedgraph.html

Specifically, make sure you specify

type=bedGraph

and that your bed file has a score in column 4

Perhaps you could post a sample (the header line, and several lines of bed format coordinates), and we can further clarify.

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written by Joseph Pearson Joseph Pearson

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