Hi Steve,
Thanks for writing back.
I re-downloaded the refGene.txt file today and was trying to grep "FSBP" from
it which is not in file but I can see it in genome browser
(chr8:95,513,351-95,518,308) NM_006550.
Thanks,
Rajesh Patidar(NIH/NCI)[C]
-----Original Message-----
From: Steve Heitner [mailto:[email protected]]
Sent: Tuesday, January 03, 2012 5:36 PM
To: Patidar, Rajesh (NIH/NCI) [C]; [email protected]
Subject: RE: [Genome] Missing genes in refGene.txt file
Hello, Rajesh.
The file you downloaded is the most current version. The RefGene table and
its associated download file are updated regularly. The version of the file
you referenced is for the human assembly hg18. I performed a search in the
Browser for MOD2 and KRC in hg18. I found no results for MOD2, but I did
find LMOD2, TMOD2 and ELMOD2. I also found no results for KRC, but I did
find KRCC1. This is consistent with the contents of the refGene.txt file
and the NCBI database.
Could you please provide a specific example of a search result that you
found in the Browser (including RefSeq ID) but did not find in refGene.txt?
Please contact us again at [email protected] if you have any further
questions.
---
Steve Heitner
UCSC Genome Bioinformatics Group
-----Original Message-----
From: [email protected] [mailto:[email protected]] On
Behalf Of Patidar, Rajesh (NIH/NCI) [C]
Sent: Friday, December 23, 2011 10:12 AM
To: [email protected]
Subject: [Genome] Missing genes in refGene.txt file
Hi,
I downloaded the the refGene.txt file from
ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/ and was looking for
a list of genes I have and wanted to know there coordinates but the list I
have, is longer than the refGene.txt's gene list.
For example I cannot find MOD2 or KRC and many more. But I can get them on
genome browser.
I am wondering where I can get the most complete list of human genes build
18 and there coordinates.
Happy Holidays,
Thanks,
Rajesh Patidar(NIH/NCI)[C]
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
_______________________________________________
Genome maillist - [email protected]
https://lists.soe.ucsc.edu/mailman/listinfo/genome
