Question: Re: About Ncbi Refseq Id
0
Jennifer Hillman Jackson ♦ 25k wrote:
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.
--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org