About tracks

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Out of date Please see the updated version of this tutorial

What is a track?

A track is the place to display your data files in JBrowse Linear View. For this tutorial we're going to add a gene track, an alignments track, and a variants track. We're just going to use basic configuration, but check the links for the track types to see what kinds of things you can configure in them.

Adding tracks

Gathering data

For genes, we'll use a GFF3 file of the NCBI RefSeq human genes. The link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz

For alignments, we're going to use on the 1000 Genomes sample NA12878. We'll use a CRAM file (BAM is also supported), and the link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram

For variants, we'll use a VCF of the 1000 Genomes variant calls (note that this VCF contains all samples, not just NA12878). The link is https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz

Creating track configurations with the CLI

jbrowse add-track https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz --name "NCBI RefSeq Genes" --category "Genes" --config '{"renderer": {"type": "SvgFeatureRenderer"}}' --skipCheck
jbrowse add-track https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram --name "NA12878 Exome" --category "1000 Genomes, Alignments" --skipCheck
jbrowse add-track https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz --name "1000 Genomes Variant Calls" --category "1000 Genomes, Variants" --skipCheck

Open "config.json" again and look at the tracks that were generated. You can see that again, it has guessed index locations for you, which you can change if needed. Create a new file called "tracks.js" and copy the tracks array into it and have it exported, like this:

tracks.js

export default [
  {
    type: 'BasicTrack',
    trackId:
      'GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff',
    name: 'NCBI RefSeq Genes',
    category: ['Genes'],
    assemblyNames: ['GRCh38'],
    adapter: {
      type: 'Gff3TabixAdapter',
      gffGzLocation: {
        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz',
        locationType: 'UriLocation',
      },
      index: {
        location: {
          uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi',
          locationType: 'UriLocation',
        },
        indexType: 'TBI',
      },
    },
    renderer: {
      type: 'SvgFeatureRenderer',
    },
  },
  {
    type: 'AlignmentsTrack',
    trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome',
    name: 'NA12878 Exome',
    category: ['1000 Genomes', 'Alignments'],
    assemblyNames: ['GRCh38'],
    adapter: {
      type: 'CramAdapter',
      cramLocation: {
        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram',
        locationType: 'UriLocation',
      },
      craiLocation: {
        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai',
        locationType: 'UriLocation',
      },
      sequenceAdapter: {
        type: 'BgzipFastaAdapter',
        fastaLocation: {
          uri: 'http://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/dna_index/Homo_sapiens.GRCh38.dna.toplevel.fa.gz',
          locationType: 'UriLocation',
        },
        faiLocation: {
          uri: 'http://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/dna_index/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai',
          locationType: 'UriLocation',
        },
        gziLocation: {
          uri: 'http://ftp.ensembl.org/pub/release-100/fasta/homo_sapiens/dna_index/Homo_sapiens.GRCh38.dna.toplevel.fa.gz.gzi',
          locationType: 'UriLocation',
        },
      },
    },
  },
  {
    type: 'VariantTrack',
    trackId:
      'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf',
    name: '1000 Genomes Variant Calls',
    category: ['1000 Genomes', 'Variants'],
    assemblyNames: ['GRCh38'],
    adapter: {
      type: 'VcfTabixAdapter',
      vcfGzLocation: {
        uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz',
        locationType: 'UriLocation',
      },
      index: {
        location: {
          uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz.tbi',
          locationType: 'UriLocation',
        },
        indexType: 'TBI',
      },
    },
  },
]

Now update "index.html" to import this file.

index.html

<html>
  <head>
    <script src="//s3.amazonaws.com/jbrowse.org/jb2_releases/jbrowse-linear-view/jbrowse-linear-view@v0.0.1-beta.0/umd/jbrowse-linear-view.js"></script>
  </head>

  <body>
    <h1>We're using JBrowse Linear View!</h1>
    <div id="jbrowse_linear_view"></div>
    <script type="module">
      import assembly from './assembly.js'
      import tracks from './tracks.js'
    </script>
  </body>
</html>