Kanwar

On Fri, Jul 20, 2012 at 8:00 PM, Jennifer Jackson <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

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

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

http://lists.bx.psu.edu/

--
Jennifer Jackson
http://galaxyproject.org