where to get the gene annotations for the latest build 37 - for plotting regional association plot

Question

[iphoenix2100]

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

[Emily]

What species?

[iphoenix2100]

Human.. Thanks

[Emily]

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

[iphoenix2100]

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

[Emily]

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.

Answer 1

[NB]

you can use refFlat from UCSC