Question: where to get the gene annotations for the latest build 37 - for plotting regional association plot
0
gravatar for iphoenix2100
3.1 years ago by
iphoenix210030
European Union
iphoenix210030 wrote:

Hi all,

I need to plot regional association plot using the R packages GAP - by using the function asplot( )

- for which in addition to the INPUT file (with pval and rsq) , i need to provide the MAP file containing information on genetic map...

- I have all these data for the genome build 37 and i need the GENE annotations file in the same build ideally.

I can find the file for build 35 but not for 37... can someone point me to the right direction.

For info: these are the columns need to be in the GENE annotations file (start, stop, strand, Gene)

 

Thanks in advance

 

sequencing assembly gwas R • 1.1k views
ADD COMMENTlink modified 3.1 years ago by Nandini430 • written 3.1 years ago by iphoenix210030

What species?

ADD REPLYlink written 3.1 years ago by Emily_Ensembl14k

Human.. Thanks

ADD REPLYlink written 3.1 years ago by iphoenix210030

Just so you know, 37 is not the latest build, that's GRCh38.

ADD REPLYlink modified 3.1 years ago • written 3.1 years ago by Emily_Ensembl14k

Thanks for the info - As our data was generated with the build 37, trying to use the same build !!

How much it will change if i use the new build (just curious) and thanks for spotting it

 

ADD REPLYlink written 3.1 years ago by iphoenix210030
1

Oh yes, use the same build as your data. Just letting you know that it wasn't the latest. GRC have a blog on the changes between the two builds. We had a blog series in Ensembl on all the things we had to do to update. Essentially, if you're using genomic coordinates, stick with what you've got. If you're using gene/variant etc IDs, you can move to the new one.

ADD REPLYlink written 3.1 years ago by Emily_Ensembl14k
2
gravatar for Nandini
3.1 years ago by
Nandini430
UCL, London
Nandini430 wrote:

you can use refFlat from UCSC

ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Nandini430
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