Track for Coverage 2018 about genoverse

[simonbrent]

Hi,

I don't entirely follow your description, but it sounds like you want the BIGWIG track. Rather than using a large WIG file, you can create a BIGWIG file using a conversion tool:

https://genome.ucsc.edu/goldenpath/help/bigWig.html
https://www.encodeproject.org/software/wigtobigwig/

Sorry, I can't help you with actually using the tool, as I have no experience of it.

With regard to question 2, I don't know if that is possible. What are you trying to achieve?

[MrKevinDC]

Hi again Simon,
Well it seems now that indeed BIGWIG will be all we need as they have now provided us with genomic bams. However another track still requires accessing data from another file:

-We have a .gff with transcript IDs and positions, and on the other hand we have a .txt with transcript IDs and gene expression values (all calculated with RSEM). We have to fetch the transcript positions from the .gff so that we can plot the values of the .txt in the browser. We thought that maybe we could load both files at once similar to how the bam/bai and vcf/tbi is done, but maybe we require a more expert insight on this.
Kind regards
Kevin

[simonbrent]

Yes, you can load both files at once. You will have modify the fileDrop plugin a bit (currently it treats the second file as an index, e.g. bam/bai), and create a new Track.Model.File extension, which has a getData function whose promise resolves once both files' data has been read. The following is untested code which should do what you want there.

getData: function (chr) {
  var model = this;

  if (this.isLocal && this.dataFiles) {
    return Promise.all(this.dataFiles.map(function (file) {
      return new Promise(function (resolve) {
        var reader = new FileReader();

        reader.onload = function (e) {
          resolve(e.target.result);
        };

        reader.readAsText(file);
      });    
    })).then(function (filesData) {
      // filesData is an array whose elements contain the contents of each file
      var combinedData = [ do something with filesData to turn it into an array of Genoverse-compatible features ]
      model.receiveData(combinedData, chr, 1, model.browser.getChromosomeSize(chr));
    });
  } else {
    return this.base.apply(this, arguments);
  }
},

[MrKevinDC]

Thank you so much Simon this is what we were struggling with now but you have painted a great picture of what we have to do. You are doing a great job supporting Genoverse, thank you.
Kind regards