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 <j...@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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> --
> Jennifer Jackson
> http://galaxyproject.org
>
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