Flaking Regions Across Tss

Question: Flaking Regions Across Tss

6.4 years ago by

United States

shamsher jagat • 590 wrote:

I am interested in getting regions flanking TSS, I am using Glaxaxy and have downloaded TSS sites using this post steps https://lists.soe.ucsc.edu/pipermail/genome/2011-June/026175.html Now what I would like to do is to get 5000 bp upstream an downstream using flank tool in galaxy, but i realize it only gave me option for gene start or whole gene. Is it possible to extract 5000 bp upstream and downstream regions across tss start site . Once I have that then I want to find non overlaping genes in my regions from chipseq data. Thanks Kanwar

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modified 6.4 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.4 years ago by shamsher jagat • 590

6.4 years ago by

Brooke Rhead • 10

Brooke Rhead • 10 wrote:

Hi Kanwar, We are unable to provide support for the tools at Galaxy. I see you have copied them on your email, so you will probably hear from them soon. If you have further questions regarding the Genome Browser, please contact us again at genome@soe.ucsc.edu. -- Brooke Rhead UCSC Genome Bioinformatics Group

ADD COMMENT • link written 6.4 years ago by Brooke Rhead • 10

6.4 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Hello Kanwar, The "Region:" options are: 1 - around start - meaning interval start coordinate 2 - around end - meaning interval end coordinate 3 - whole gene - meaning entire intervals Pick option #1. The "Location of the flanking region/s:" options are: 4 - Upstream 5 - Downstream 6 - Both Pick option #6 with "Length of the flanking region(s):" set to 5000. Once I have that then I want to find non overlaping Do you want to identify/label known genes or discover novel genes? This part of your question is not clear. Could you explain in more detail the end goal? It is likely some for of the tool "Operate on Genomic Intervals - > Merge will do what you want", but it is difficult to recommend the correct option. Going forward, sending question to a single public list, as Brooke also suggests, is best. It is generally considered a good idea to not post to two or more, at the same time, with the same email to start threads. Thanks! jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.4 years ago by Jennifer Hillman Jackson ♦ 25k

I want to have list of genes from UCSC browser or known genes. Thanks Kanwar

ADD REPLY • link written 6.4 years ago by shamsher jagat • 590

Hello, To summarize, you want to find existing genes that: 1 - have overlap with your ChIP-seq dataset 2 - have overlap within 5000 bp upstream of known TSS intervals The basic steps are: a - obtain intervals for TSS b - obtain intervals for ChIP-seq peaks c - obtain intervals for existing genes (transcripts) d - answer both #1 & #2 above by comparing a + b, then the result + c using tools from the group "Operate on Genomic Intervals" plus other data manipulation tools as needed For a, this was the prior question/reply. For b, please see: http://main.g2.bx.psu.edu/u/james/p/exercise-chip-seq http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012 -> Prot 3 For c, this is in the UCSC mailing list post, but also in several Protocols of the Using Galaxy paper. For d, see Prot 1 in the Using Galaxy paper for how to identify common regions to address question #1. Prot 4 walks through all Genomic Interval tools, plus the tools themselves have example graphics. Hopefully this helps, Jen Galaxy team -- Jennifer Jackson http://galaxyproject.org

ADD REPLY • link written 6.3 years ago by Jennifer Hillman Jackson ♦ 25k

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