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).
Question: How to get all the versions of refSeq
4.6 years ago by
talmud.k • 0
talmud.k • 0 wrote:
ADD COMMENT • link •
3.4 years ago by
Reece • 250
Reece • 250 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 COMMENT • link
Please log in to add an answer.
Powered by Biostar version 2.3.0
Traffic: 2072 users visited in the last hour