Question: Is there anyway to get the gene fullname and shortname in the same time?
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gravatar for Xiaohan Pan
2.4 years 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 • 504 views
ADD COMMENTlink modified 2.4 years ago by Pierre Lindenbaum124k • written 2.4 years ago by Xiaohan Pan10
2
gravatar for Pierre Lindenbaum
2.4 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum124k wrote:

NCBI gene info file ? ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz

ADD COMMENTlink written 2.4 years ago by Pierre Lindenbaum124k

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

ADD REPLYlink modified 2.4 years ago • written 2.4 years ago by Xiaohan Pan10
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