Question: How to get all the versions of refSeq
0
gravatar for talmud.k
4.2 years ago by
talmud.k0
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 • 1.6k views
ADD COMMENTlink modified 3.0 years ago by Reece250 • written 4.2 years ago by talmud.k0

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

ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene/LRG_RefSeqGene

ADD REPLYlink written 4.1 years ago by carterc10
0
gravatar for Reece
3.0 years ago by
Reece250
United States
Reece250 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 written 3.0 years ago by Reece250
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