Question: How to convert HOMER's motif results to gene ID
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gravatar for tejaswi.iyyanki
2.6 years ago by
tejaswi.iyyanki0 wrote:

I have list of homer results. For example:

CTCF(Zf)/CD4+-CTCF-ChIP-Seq(Barski_et_al.)/Homer

I usually extract the first letters using pattern - CTCF.

But there are several others where I cannot readily extract the gene ID. For example:

GATA(Zf),IR3/iTreg-Gata3-ChIP-Seq(GSE20898)/Homer

Is there a way to convert all these homer motif results into gene ID so that I can easily overlay fpkm values or differential expression of genes into homer results?

I am interested in selecting motifs whose gene is expressed.

Thanks!

chip-seq atac-seq motif homer • 1.4k views
ADD COMMENTlink modified 2.6 years ago by geek_y9.3k • written 2.6 years ago by tejaswi.iyyanki0

As there is no specific pattern to extract only the gene id, quick thing I can think of is to use python or perl to match (regex) all the gene names ( from a list of gene names) against the homer output and extract the matched portion along with the other information you need.

ADD REPLYlink modified 2.6 years ago • written 2.6 years ago by geek_y9.3k
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