Finding Gene names from chromosome positions whilst maintaining fold change and p and q values
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4.5 years ago
benjyrolls ▴ 70

hi

I have a peaks interval output from MACS2.1 which is attached below.

How do I find the gene names using the start and end positions, whilst maintaining the fold change values in Galaxy in my file attached below?

I have followed other posts on the forum such as this one but this does return only gene names without the expression values(fold change, p-value, etc)

http://tinypic.com/view.php?pic=1zb4sw&s=9

ChIP-Seq macs Galaxy • 1.1k views
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there are plenty of chip-seq peak annotation tools that you can you. You can use PAVIS, Chip-Seq anno ,chipseek, HOMER But the bedtools is simply fine. You can later also us

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4.5 years ago

Use "bedtools nearest" (or a tool specifically for "peak annotation", though frankly bedtools gets the job done).

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