Question: How to go back to sequences from MACS2 peaks
0
gravatar for dorota.komar
8 months ago by
dorota.komar10
Spain
dorota.komar10 wrote:

Hi,

I am playing with my ChIP-seq results. I would like to check if I have any overrepresented motifs in the places my transcriptor factor is binding. To do that I have to have sequences of the MACS2. Is there any easy way of doing that in galaxy? Like overlapping once again mapped sequenced from bowtie with MACS2 results and only have the sequences significantly enriched/bound by my TF? In another way I would like to get the sequences from genome coordinates for Arabidopsis - I have seen there is an easy way of doing that for human genome, but I cannot find any way of doing that for Arabidopsis...

Thanking you in advance!

Dorota

ADD COMMENTlink modified 8 months ago by Devon Ryan1.9k • written 8 months ago by dorota.komar10
0
gravatar for Devon Ryan
8 months ago by
Devon Ryan1.9k
Germany
Devon Ryan1.9k wrote:
  1. Use the "GetFastaBed" tool with your peaks to get a fasta file with an entry for each peak.
  2. Use "MEME" on that.
ADD COMMENTlink written 8 months ago by Devon Ryan1.9k
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