Question: Motif discovery-Chip seq
0
gravatar for mayurdoke
13 months ago by
mayurdoke10
mayurdoke10 wrote:

Hello,

I am analyzing ChIP-Seq data from Illumina using Galaxy web server. I mapped the reads with bowtie2 tool and did the peak calling with MACS2. The next thing I did is to annotate the peaks with genomic regions i.e. promoter, intergenic, intron etc and gene names. The output looks like picture below- enter image description here

After this, I have used the peak region coordinates to convert into fasta format. Then, I used the Fasta format file of these peak regions to analyze and discover significant motifs with the help of MEMEChIP tool. I have got the following file- enter image description here

Now my question is that the 4th column- Known or Similar Motifs represents gene names are transcription factor binding to particular motif or genes consists of these particular significant motifs? Thank you.

chip-seq • 619 views
ADD COMMENTlink modified 13 months ago • written 13 months ago by mayurdoke10
0
gravatar for Jennifer Hillman Jackson
13 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hi,

These are motifs, not genes.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 13 months ago by Jennifer Hillman Jackson25k
0
gravatar for mayurdoke
13 months ago by
mayurdoke10
mayurdoke10 wrote:

Thank you very much for your help !!!!!!!!

ADD COMMENTlink written 13 months ago by mayurdoke10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 152 users visited in the last hour