Question: [Genome] Genome-Wide Dataset Of Protein Location Conversion
0
Manuel Leichsenring • 20 wrote:
Hi Dana,
the way I do it, is the following:
Get a list of all genes (e.g. RefSeq) using the "Get Data" "From UCSC
Main Tablebrowser" option.
"Get Flanks" of the genes (in your case 1kb or 5kb).
Use "Join" from "Operate on genomic intervals" to intersect your peak
regions with a) Upstream Flanks b) Downstream Flanks c) the genes
themselves.
You can then use the "Group" option and "Concatenate queries" to get a
single list of genes without duplicates.
Cheers
Manuel
Good Afternoon Dana:
You could produce such a list from a given position with a MySQL
operation
to the UCSC public MySQL server. Note this Wiki page with a
description
of the command:
http://genomewiki.ucsc.edu/index.php/Finding_nearby_genes
--Hiram
To: galaxy-user@lists.bx.psu.edu
Subject: [galaxy-user] FW: [Genome] Genome-wide dataset of protein
location conversion
Hello,
We have been trying to determine a method to convert ChIP-Seq
coordinates into a list of genes and are wondering the best way to
utilize the Galaxy browser. The UCSC folks suggested you could help
but I should have been more specific with my request. Ideally we would
like to take global binding coordinates and find out what genes are
nearby (ie at either a 1 or 5kb) instead of simply the âclosest
featureâ. Might you be able to advise on this? I have enclosed
the text (.bed format) file I used to get the binding sites in the
UCSC genome browser. Thanks in advance!
Cheers,
Dana
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