Hello,
If you want to just link on the accession ID, one way to do this would
be to pull over the RefSeq track data from the UCSC Table browser. Since
you may be accessing very large tables (such as gbCdnaInfo), use the
mirror BX Main under "Get Data".
- In the Table browser, navigate to the RefSeq Genes track (making
sure that region = genome).
- If the gene accessions are RefSeq accession IDs, just use the RefSeq
Genes primary table refGene.
- If the accessions are mRna or another type, then for output select
"selected fields from primary and related tables". On the next form,
tables of interest that may include your version of the gene ID include
refLink and gbCdnaInfo. Check all of the refGene table fields (for the
genomic coordinates) and add in the linking identifier that matches your
IDs. Submit and send the data to Galaxy.
- Once in Galaxy, use "Join, Subtract and Group -> Join two Datasets
side by side on a specified field" using the accession as the join field.
If you have global genomic coordinates and want to pull out any genes
(full coordinates) that may be related, explore the tools under "Operate
on Genomic Intervals". The results will not be as specific, but may
still be interesting, especially the "Profile Annotations for a set of
genomic intervals" tool (human only).
Similar operations can be done using the UCSC Genes table linked with
the kgXref or kgAlias table.
Best wishes for your project,
Jen
Galaxy team
On 3/16/11 1:49 PM, shamsher jagat wrote:
Is it possible to extract genomic coordinates If I have gene accession
ID Chr stat and end position. Any pointer will be helpful.
Thanks.
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
