Intersect - UCSC Genome Browser

[Kassi Kosnicki]

Hi there, 

I was wondering if you might be able to help me analyze my ChIP-seq data. I've created a custom track in the narrowPeak format. I have pasted the example below. I have looked through much of the documentation and have searched through the FAQs and your mailing list archive trying to find a solution to my issue. 

Currently, I am trying to expand my peak region by 100kb downstream and upstream of the peak and then intersect this region with the hg10refseq to identify genes that are surrounding these peaks. When selecting the 'intersect' parameter int the Genome Table Browser, I notice that you can choose regions N bases upstream or downstream of the start/end but not both. However I'm trying to create this spanned region overall. Is there a tool in the UCSC Browser I can use to span this peak region, then identify the corresponding genes by intersecting?

Also, I've tried to intersect other files and output to Galaxy, however the output throws an error saying it can not be in HTML format. Which output should I select?

Thank you for your time,

Kassi 

 

Kassi Kosnicki

Associate Computational Biologist

Department of Medicine

UC San Diego | 9500 Gilman Drive, MC 0765 l La Jolla, CA 92093 

Email: kkos...@cloud.ucsd.edu

Office: (858)246-2403

[Cath Tyner]

Hi Kassi,

Thanks for using the UCSC Genome Browser and for asking about adding bases to upstream and downstream regions. Unfortunately, as you noted, our Table Browser can only expand regions in one direction at a time. Also, the Table Browser is currently unable to send narrowPeak format to Galaxy, and it is also unable to convert it to a BED3 file (as an option in the "output" format. This is something that will be updated, and I will make a note to let you when this type of support is enabled. 

For now, I would suggest the following:

One possibility is to convert your narrowPeak to a BED3  (using 'cut' or 'awk'), and then use Galaxy's SlopBed tool  (either by uploading your file to their online tool, or by using their command line version) to accomplish your goal of expanding your regions in both directions. One you have the new coordinates, you could append your other fields, thus creating the narrowPeak format. You could then use your revised narrowPeak file with expanded regions to intersect with overlapping hg19 genes in the UCSC Genome Browser.

Please respond to this list if you have further questions!

Thank you again for your inquiry and for using the UCSC Genome Browser. 

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. . .

Cath Tyner

UCSC Genome Browser, Software QA & User Support

UC Santa Cruz Genomics Institute

UCSC Genome Browser

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