Gencode v36

[s-paquette]

With the Genomics Data Commons moving to Gencode v36, are there plans to make the v36 annotation available in the AWS bucket?

[jrobinso]

Updates such as this are done by request, I will assume this is a request for the "hg38" assembly.

We aren't connected to the "Genomics Data Commons" project

[s-paquette]

Understood. Yes, a request for Genocode v36 HG38, when you have a chance. Thank you!

[jrobinso]

v40 is the latest version.

[jrobinso]

@s-paquette I'm a bit confused by your request, why do you specifically reference the AWS bucket?

[s-paquette]

That's where the examples in the Wiki show it:

{
      name: "Genes",
      type: "annotation",
      format: "bed",
      sourceType: "file",
      url: "//igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed",
      indexURL: "//igv.broadinstitute.org/annotations/hg19/genes/gencode.v18.collapsed.bed.idx",
      displayMode: "EXPANDED"
    }

We had previously been pointed to https://s3.amazonaws.com/igv.broadinstitute.org/annotations/hg38/genes/gencode.v24.annotation.sorted.gtf.gz (where previously was some years ago), so I wanted to check and find out if these were still being offered.

[jrobinso]

Oh thanks, I'll update the wiki example. We host some tracks for convenience, but unlike for example UCSC hosting data is not a primary goal of this project, files move from time to time and even get deleted as we don't have unlimited storage.

Having said that I'll be updating our hosted set to include v36 and v40.

[jrobinso]

This request really doesn't apply to igv.js, which is just the javascript component. Moving to igv-webapp.

[jrobinso]

I've added v36 and v40 to the "Annotations" menu for hg38, this will appear in the next webapp release.