Hello Shibu,
The refGene.txt table from UCSC (file from downloads or as extracted
using their Table browser), contains the current RefSeq transcripts for
mouse, from NCBI, if they align with BLAT to the mouse genome (most
should). So the issue is likely with your input list's content.
Some things to check:
- are there older versions of sequences mixed in with the new
(duplicates - check the ".N" versioning)
- are all sequences still active (none are deleted)?
- maybe not all sequences are mouse?
You could explore the "Other RefSeq" track at UCSC if you want to find
out about RefSeq sequences from other species, in the context of an
alignment to the mouse genome.
- if sequence is active, most current, mouse, and not in list - try
running a quick web-BLAT at UCSC. If it doesn't align, and you cannot
tell why, the best thing to do is to ask them directly why the alignment
failed at gen...@ucsc.edu. Sequence quality may be an issue (Genome or
RefSeq), but they can help with the exact why.
Hopefully this helps!
Thanks,
Jen
Galaxy team
ps. Next time, for data questions, please use galaxy-u...@bx.psu.edu.
Any non-confidential follow-up should also post back to the list so the
entire team and subscribers can offer input/learn.
On 2/4/11 9:22 AM, Shibu John wrote:
Hi Jen,
I have a list of (36692) NCBI refSeq id in the following format. (Mouse )
*****
gi|10048421|ref|NM_020488.1|
gi|10048425|ref|NM_020501.1|
****
Is there any way to get the chromosome start position of these geneID
with Galaxy?
I tried to intersect with the "NM_" id with UCSC
"http://hgdownload.cse.ucsc.edu/goldenPath/mm9/database/refGene.txt.gz";
********
gi|10048425|ref|NM_020501.1| Tas2r105 NM_020501 chr6
- 131636578 131637481
********
But this "refGene.txt" contains only 28108 id's..
It will be a great help that if you can help me to get the chromosome
start position of these genes.
Thanks,
Shibu
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
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