Finding Gene names from chromosome positions whilst maintaining fold change and p and q values
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)
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Devon Ryan
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benjyrolls
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benjyrolls
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Use "bedtools nearest" (or a tool specifically for "peak annotation", though frankly bedtools gets the job done).
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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