Question: Excluding promoter and exon peaks
0
gravatar for mdp07vm
24 months ago by
mdp07vm20
United States
mdp07vm20 wrote:

Hi, would appreciate if someone could advise me on how to exclude promoter and exon peaks after peak calling. I've performed a TF chip-seq and did the peak calling using HOMER. For the next part of my analysis, I wish to focus only on intergenic and intronic regions for data intersection study with another set of hi-seq data. Hence, the need to exclude the promoter and exon peaks. FYI, I've done the peak calling using HOMER.

Thanks,

Victor

chip-seq • 676 views
ADD COMMENTlink modified 24 months ago by Jennifer Hillman Jackson25k • written 24 months ago by mdp07vm20
1
gravatar for Jennifer Hillman Jackson
24 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There are a few ways to do this, one is BedTools > SubtractBed.

The source for the reference data (the regions to subtract) can vary depending on the genome build you are working with. If by chance working with a genome hosted by UCSC, the tool Get Data > UCSC Main is a simple way to obtain reference data representing promoter/exon regions.

Best, Jen, Galaxy team

ADD COMMENTlink written 24 months ago by Jennifer Hillman Jackson25k

Hi Jen,

Thanks for the suggestions. I'm working with mm9 hosted by UCSC. I tried the Get Data>UCSC Main method, but I'm struggling to find the track (or tracks) that represents promoters/exons. It will be terrific if you can point me to the correct track/s. Appreciate your help in this!

Thanks,

Victor

ADD REPLYlink written 24 months ago by mdp07vm20
1

I think I just found out how to do this. I will let you know if I encounter any problems. Thanks.

ADD REPLYlink written 24 months ago by mdp07vm20
1

Glad you have this going! For others, try tracks in the UCSC Table browser under "Gene and Gene Predictions". Select "Bed" output and submit. The next form allows one to specify specific regions types (exon, introns, promoters, user-specified region extensions, and more). Submit that form and the data will load into Galaxy (when using the Get Data > UCSC Main tool or if the "Submit to Galaxy" box is checked).

"Refseq Genes" is a good place to start yet explore others (Ensembl, etc) to find the right fit for your project.

ADD REPLYlink modified 24 months ago • written 24 months ago by Jennifer Hillman Jackson25k
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