Question: Motif discovery-Chip seq
0
gravatar for mayurdoke
9 weeks ago by
mayurdoke0
mayurdoke0 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 • 123 views
ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by mayurdoke0
0
gravatar for Jennifer Hillman Jackson
9 weeks ago by
United States
Jennifer Hillman Jackson23k wrote:

Hi,

These are motifs, not genes.

Hope this helps! Jen, Galaxy team

ADD COMMENTlink written 9 weeks ago by Jennifer Hillman Jackson23k
0
gravatar for mayurdoke
9 weeks ago by
mayurdoke0
mayurdoke0 wrote:

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

ADD COMMENTlink written 9 weeks ago by mayurdoke0
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