Question: Finding Gene names from chromosome positions whilst maintaining fold change and p and q values
gravatar for benjyrolls
2.9 years ago by
benjyrolls70 wrote:


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)

chip-seq galaxy macs • 884 views
ADD COMMENTlink modified 2.9 years ago by Devon Ryan94k • written 2.9 years ago by benjyrolls70

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

ADD REPLYlink written 2.9 years ago by ivivek_ngs4.9k
gravatar for Devon Ryan
2.9 years ago by
Devon Ryan94k
Freiburg, Germany
Devon Ryan94k wrote:

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

ADD COMMENTlink written 2.9 years ago by Devon Ryan94k
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