alexander-veit/higlass-pileup

HiGlass Pileup Track

Viewer for sequence alignments.

Note: This is the source code for the pileup only! You might want to check out the following repositories as well:

• HiGlass viewer: https://github.com/higlass/higlass
• HiGlass server: https://github.com/higlass/higlass-server
• HiGlass docker: https://github.com/higlass/higlass-docker

Installation

npm install higlass-pileup

Usage

The live scripts can be found at:

• https://unpkg.com/higlass-pileup/dist/higlass-pileup.min.js

Client

1. Make sure you load this track prior to hglib.js. For example:

<script src="/higlass-pileup-track.js"></script>
<script src="hglib.js"></script>
<script>
  ...
</script>

2. Now, configure the track in your view config and be happy!

{
  "editable": true,
  "trackSourceServers": [
    "http://higlass.io/api/v1"
  ],
  "exportViewUrl": "/api/v1/viewconfs",
  "views": [
    {
      "initialXDomain": [
        0,
        100000
      ],
      "tracks": {
        "top": [
          {
            "type": "pileup",
            "options": {
              "axisPositionHorizontal": "right",
              "axisLabelFormatting": "normal",
              "showCoverage": false,
              "colorScale": [
                // A T G C N Other
                "#2c7bb6",
                "#92c5de",
                "#ffffbf",
                "#fdae61",
                "#808080",
                "#DCDCDC"
              ]
            },
            "height": 180,
            "uid": "FylkvVBTSumoJ959HT4-5A",
            "data": {
              "type": "bam",
              "url": "https://pkerp.s3.amazonaws.com/public/bamfile_test/SRR1770413.sorted.bam",
              "chromSizesUrl": "https://pkerp.s3.amazonaws.com/public/bamfile_test/GCF_000005845.2_ASM584v2_genomic.chrom.sizes"
            },
            "width": 470
          }
        ]
      },
      "layout": {
        "w": 12,
        "h": 6,
        "x": 0,
        "y": 0
      }
    }
  ]
}

3. To use in higlass.io:

• Modify the viewconf above to specify the URL for your BAM file.
• Either remove or update the chromSizesUrl entry to point to a chromosome sizes file for the assembly that your BAM file is aligned to. If it's omitted, the chromosome sizes will be extracted directly from the BAM file and ordered best-guess semantically (i.e. chr1, chr2, ...., chrM, chrX, chrY).
• Save the viewconf as a JSON file.
• Navigate to higlass.io/app and drag the JSON file onto the viewer.
• Browse away!

Support

For questions, please either open an issue or ask on the HiGlass Slack channel at http://bit.ly/higlass-slack

Development

Installation

$ git clone https://github.com/higlass/higlass-pileup-track && higlass-pileup-track
$ npm install

Commands

Developmental server: npm start Production build: npm run build