Question: How to get all the versions of refSeq
gravatar for talmud.k
5.7 years ago by
talmud.k0 wrote:

I have downloaded some databases to make an annotation of my sequencing results. But I found that sometimes there is only the HGVS description of some variations rather than the genomic positions. When I want to extract the positions of them in the refGene (downloaded from UCSC), I found that there have no version numbers of the gene IDs. The description in my database is like "NM_144631.5:c.1015T>C", and the ID in refGene is just "NM_144631". I check them in the NCBI website, it's really the latest version. While I doubt that there maybe have some old data that corresponds to the older version in my databases. So how can I get all the versions of the refSeq data, containing the information about the position, cDNA, and exon regions (just like that in the refGene).

gene • 2.4k views
ADD COMMENTlink modified 4.4 years ago by Reece270 • written 5.7 years ago by talmud.k0

Im looking for the same thing, i only found the file for the current assembly... does this help any

ADD REPLYlink written 5.5 years ago by carterc10
gravatar for Reece
4.4 years ago by
United States
Reece270 wrote:

Consider the Python hgvs package. [Disclosure: I'm one of the authors.]

hgvs uses UTA, the Universal Transcript Archive, which is a collection of transcript versions from multiple sources with alignments to multiple references.

ADD COMMENTlink modified 4 months ago by RamRS26k • written 4.4 years ago by Reece270
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1139 users visited in the last hour