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

On 7/23/12 7:33 AM, shamsher jagat wrote:

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

Thanks

Kanwar

On Fri, Jul 20, 2012 at 8:00 PM, Jennifer Jackson <jen@bx.psu.edu mailto:jen@bx.psu.edu> wrote:

Hello Kanwar,


On 7/20/12 3:31 PM, shamsher jagat 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
    <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.


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.


    Is it possible to extract 5000 bp upstream and downstream
    regions across
    tss start site .


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

    genes in my regions from chipseq data.


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


    Thanks

    Kanwar



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