Query!!!

6 views

Skip to first unread message

Smriti Mishra

unread,

Sep 3, 2015, 11:37:49 AM9/3/15

to gen...@soe.ucsc.edu

Hello UCSC GB support,

I have list of some gene names. The names are ref genes.

All i want to generate is a file such as this
chromosome start_of_gene end_of_gene gene_name strand

For example i have a gene

PDCD11

Its coordinates are
chr10 105156412 105206019 PDCD11 +

How can i get this for 20 - 30 genes all together.

These are ref genes.

Note: Same question asked by another person in 2013. I tried to follow the same steps but not getting results kindly help me out!!!

Sincerely,

Smriti Mishra

robert kuhn

unread,

Sep 4, 2015, 4:52:55 PM9/4/15

to Smriti Mishra, gen...@soe.ucsc.edu, ku...@soe.ucsc.edu

Hello, Smriti,

We recently released a video that addresses this very question.
Please see the first video on our training/video page:

http://genome.ucsc.edu/training/vids/index.html#vid01

The transcript is available as well. The process would be the
same for the RefSeq Genes track, using the RefGene table. The
main difference would be that you would want to load your list into
the Table Browser using "identifiers: [ paste list ] button" instead
of choosing genomic coordinates to restrict your query. Be sure
to select "region: genome" because the list is likely to span
multiple chromosomes.

I hope this addresses your question. If not, please respond to the
list with a followup.

thanks for using the Genome Browser

--b0b kuhn
ucsc genome bioinformatics group