match ucsc and ncbi transcript identifiers

Question

[User6891]

Hi,

I want, for all ucsc transcript identifiers (format "uc0000.0"), the corresponding NCBI transcript identifiers (format "NM_0000.0).

Is there a way to obtain this from the ucsc or ncbi website?

Answer 1

[Pierre Lindenbaum]

In knownToRefSeq

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/knownToRefSeq.txt.gz" | gunzip -c | head
uc032mzh.1    NM_001282321
uc032mze.1    NR_004430
uc032mzi.1    NR_037446
uc032kdk.2    NM_001100122
uc032kdl.2    NM_014963
uc061ytg.1    NM_004518
uc061yth.1    NM_172108
uc032pqf.2    NM_004518
uc032pqd.2    NM_172108
uc061yti.1    NM_172108