Where can I find an annotation table for human gencode ensemble gene ids to gene name/description?
1
0
Entering edit mode
2.2 years ago
O.rka ▴ 710

All of the resources on BioStars and Ensembl I am seeing require me submitting lists to some REST or server. Is there anywhere I can just download the raw annotation table?

I am using hg38 v39 http://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/

I'm looking for a table that has, at the very least, [gene id]<sep>[gene symbol]<sep>[full gene name]

fastq annotation genomics rnaseq • 975 views
ADD COMMENT
0
Entering edit mode

you can use ensembl+biomart without a list of identifiers.

ADD REPLY
0
Entering edit mode

Do you have a link out to any tutorials by any chance?

ADD REPLY
2
Entering edit mode
2.2 years ago
GenoMax 141k

BioMart --> Ensembl Genes --> Human Genes --> Attributes (in left column) --> Select Gene Stable ID, Gene Name, Gene Description (or anything else you want, right pane) --> Hit Count --> 68005 as of today --> Results ----> (Choose if you need unique ones) --> Send to File --> Choose format (TSV,CSV etc) --> Provide file name.

ADD COMMENT

Login before adding your answer.

Traffic: 1855 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6