Question: Is there anyway to get the gene fullname and shortname in the same time?
gravatar for Xiaohan Pan
21 months ago by
Xiaohan Pan10
Xiaohan Pan10 wrote:

I did denovo of a kind of fish , it has no ref, so I only get lots of predicted genenames, like: (PREDICTED: uridine phosphorylase 2 isoform X1 [Astyanax mexicanus], PREDICTED: TBC1 domain family member 2A [Anolis carolinensis]) Some contains abbreviation, but some haven't, but I need to convert these fullname into abbreviation like "TBC1", in order to do pathway or kegg.

I want to know if there is a file contains both the full and abbreviated name? I can find a fine ensemblToGeneName.txt.gz contains abbreviation, but I can't a file contains full name, and it's impossible for me to search them one by one on the Internet, I have thousands fullname need to convert.

Your suggestion will be appreciated!

rna-seq gene genome • 411 views
ADD COMMENTlink modified 21 months ago by Pierre Lindenbaum118k • written 21 months ago by Xiaohan Pan10
gravatar for Pierre Lindenbaum
21 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum118k wrote:

NCBI gene info file ?

ADD COMMENTlink written 21 months ago by Pierre Lindenbaum118k

Thank you, and I found a R package mygene It's great! It solved my problem, and this is the manual

ADD REPLYlink modified 21 months ago • written 21 months ago by Xiaohan Pan10
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: 1467 users visited in the last hour