Excluding promoter and exon peaks

Question: Excluding promoter and exon peaks

2.3 years ago by

United States

mdp07vm • 20 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 • 887 views

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modified 2.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 2.3 years ago by mdp07vm • 20

2.3 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k 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 COMMENT • link written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

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 REPLY • link written 2.3 years ago by mdp07vm • 20

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

ADD REPLY • link written 2.3 years ago by mdp07vm • 20

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 REPLY • link modified 2.3 years ago • written 2.3 years ago by Jennifer Hillman Jackson ♦ 25k

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