Gosling Data Transformation Example: Filtering reads from an indexed BAM file based on MAPQ score

README.md

Gosling Data Transformation Example

Filter reads from an indexed BAM file based on MAPQ score

Created with help by @sehilyi

gosling.js

{
  "title": "Filtering Reads Based on MAPQ Scores",
  "subtitle": "",
  "static": false,
  "layout": "linear",
  "centerRadius": 0.05,
  "xDomain": {"chromosome": "1", "interval": [136750, 139450]},
  "spacing": 0.01,
  "tracks": [
    {
      "alignment": "overlay",
      "title": "Original Coverage",
      "data": {
        "type": "bam",
        "url": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam",
        "indexUrl": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam.bai",
        "loadMates": true
      },
      "mark": "bar",
      "tracks": [
        {
          "dataTransform": [
            {"type": "coverage", "startField": "start", "endField": "end"}
          ],
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "y": {"field": "coverage", "type": "quantitative", "axis": "right"},
          "color": {"value": "#C6C6C6"}
        }
      ],
      "width": 1250,
      "height": 80
    },
    {
      "alignment": "overlay",
      "title": "Original Reads",
      "data": {
        "type": "bam",
        "url": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam",
        "indexUrl": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam.bai",
        "loadMates": true,
        "maxInsertSize": 300
      },
      "mark": "rect",
      "tracks": [
        {
          "dataTransform": [
            {
              "type": "displace",
              "method": "pile",
              "boundingBox": {
                "startField": "start",
                "endField": "end",
                "padding": 5,
                "isPaddingBP": true
              },
              "newField": "pileup-row"
            }
          ],
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "color": {
            "field": "mapq",
            "type": "quantitative",
            "legend": true
          }
        }
      ],
      "tooltip": [
        {"field": "start", "type": "genomic"},
        {"field": "end", "type": "genomic"},
        {"field": "insertSize", "type": "quantitative"},
        {"field": "mapq", "type": "quantitative"},
        {"field": "svType", "type": "nominal"},
        {"field": "strand", "type": "nominal"},
        {"field": "numMates", "type": "quantitative"},
        {"field": "mateIds", "type": "nominal"}
      ],
      "row": {"field": "pileup-row", "type": "nominal", "padding": 0.2},
      "width": 1250,
      "height": 400
    },
    {
      "alignment": "overlay",
      "title": "Filtered Coverage (mapq = 0)",
      "data": {
        "type": "bam",
        "url": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam",
        "indexUrl": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam.bai",
        "loadMates": true
      },
      "mark": "bar",
      "tracks": [
        {
          "dataTransform": [
            { "type": "filter", "field": "mapq", "oneOf": [0] },
            {"type": "coverage", "startField": "start", "endField": "end"}
          ],
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "y": {"field": "coverage", "type": "quantitative", "axis": "right"},
          "color": {"value": "#C6C6C6"}
        }
      ],
      "width": 1250,
      "height": 80
    },    
    {
      "alignment": "overlay",
      "title": "Filtered Reads (mapq = 0)",
      "data": {
        "type": "bam",
        "url": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam",
        "indexUrl": "https://s3.amazonaws.com/gosling-lang.org/data/example_higlass.bam.bai",
        "loadMates": true,
        "maxInsertSize": 300
      },
      "mark": "rect",
      "tracks": [
        {
          "dataTransform": [
            {
              "type": "filter",
              "field": "mapq",
              "oneOf": [0]
            },
            {
              "type": "displace",
              "method": "pile",
              "boundingBox": {
                "startField": "start",
                "endField": "end",
                "padding": 5,
                "isPaddingBP": true
              },
              "newField": "pileup-row"
            }
          ],
          "x": {"field": "start", "type": "genomic"},
          "xe": {"field": "end", "type": "genomic"},
          "color": { "value": "#440154" }
        }
      ],
      "tooltip": [
        {"field": "start", "type": "genomic"},
        {"field": "end", "type": "genomic"},
        {"field": "insertSize", "type": "quantitative"},
        {"field": "mapq", "type": "quantitative"},
        {"field": "svType", "type": "nominal"},
        {"field": "strand", "type": "nominal"},
        {"field": "numMates", "type": "quantitative"},
        {"field": "mateIds", "type": "nominal"}
      ],
      "row": {"field": "pileup-row", "type": "nominal", "padding": 0.2},
      "width": 1250,
      "height": 400
    }
  ]
}