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 genome@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-user@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