Question: Ensembl id to Gene name
1
gravatar for V
4.0 years ago by
V230
UK/London
V230 wrote:

I have a normal count table with columns being the sample names and rows being Ensembl ideas, does anyone know of an easy way that I can convert all of the ensembl ids into official gene names?

Thanks

ensembl • 8.5k views
ADD COMMENTlink modified 4.0 years ago by EagleEye6.6k • written 4.0 years ago by V230
1
gravatar for igor
4.0 years ago by
igor11k
United States
igor11k wrote:

See previous discussion:

ADD COMMENTlink written 4.0 years ago by igor11k

Thanks Igor,

I meant if there is a tool on R (or a command you might be aware of) that can sort out the rows automatically. Not how to do it manually using a database. Fairly new to R and programming here so a less obtuse answer would be greately appreciated. Or the actual R code. Thanks again.

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by V230
1

https://bioconductor.org/packages/release/bioc/html/biomaRt.html

ADD REPLYlink written 4.0 years ago by igor11k
0
gravatar for datascientist28
4.0 years ago by
University of Washington
datascientist28440 wrote:

http://uswest.ensembl.org/biomart/martview/8d0c08f24137867826fc952b01798b1c

Watch the tutorial at the bottom. I think this is what you are looking for

ADD COMMENTlink written 4.0 years ago by datascientist28440

Here is a tutorial pdf http://uswest.ensembl.org/info/website/tutorials/biomart_worked_ex.pdf

ADD REPLYlink written 4.0 years ago by datascientist28440

Thanks for your help,

Ive looked at all of the tutorials, and all of these essentially show how to generate a new table that has the gene name next to the ensembl id if i'm reading all of this correctly.

What I need is how to convert the column (whose rows are made out of enseml Ids) into a column made up of the gene names, without changing the rest of the columns of the file if that makes sense?

ADD REPLYlink written 4.0 years ago by V230

My simple suggestion is download the complete annotation from UCSC as mentioned below and merge your count file with the downloaded annotation file using Ensembl id column which is common in both files (this can be done with simple UNIX 'join' command or R 'merge' function).

The UCSC annotation file will have all information like, Ensembl ID, Gene symbols, classification, etc.,

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by EagleEye6.6k

thank you!!

Sorted it all out by doing some reading on the "merge" function!!

ADD REPLYlink written 4.0 years ago by V230
0
gravatar for EagleEye
4.0 years ago by
EagleEye6.6k
Sweden
EagleEye6.6k wrote:

A: I need to download a list of all human genes with their respective Esemble gene

ADD COMMENTlink written 4.0 years ago by EagleEye6.6k
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