Question: convert alignID to gene symbol
0
gravatar for tcherlin
3.7 years ago by
tcherlin0
United States
tcherlin0 wrote:

Hello,

I have been using Galaxy to determine genes from chromosome positions. I upload large BED files into Table Browser and set the output format to "all fields in selected table". The resulting data is very useful, as it returns me with the alignIDs. I have then been individualy looking up each alignID though to find the gene symbols. This is a BIG time waster. Is there a way to convert the alignIDs to gene symbols on Galaxy? or anywhere? The output format seems pretty incompatible with a lot of the conversion websites out there.

Please help!

Tess

gene symbol convert alignid • 705 views
ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by tcherlin0
1
gravatar for fubar
3.7 years ago by
fubar1.1k
Australia
fubar1.1k wrote:

Hi, Tess.

You don't provide much detail in your question. Although it would be possible to do this using Galaxy built in text/interval file manipulation tools, my guess is that it's going to be much easier for you to add geneSymbol from the known gene table in the UCSC table browser step, as described by UCSC helpdesk staff - see: https://www.mail-archive.com/genome@soe.ucsc.edu/msg07774.html

I hope this solves your problem?

 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by fubar1.1k
0
gravatar for tcherlin
3.7 years ago by
tcherlin0
United States
tcherlin0 wrote:

Yes! Thank you so much Ross. This exactly the answer I was looking for. Sorry I did not include more information, but it seems like the problem was very easy to solve!

All the best!

ADD COMMENTlink written 3.7 years ago by tcherlin0
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