{
  "assemblies": [
    {
      "name": "hg38",
      "aliases": ["GRCh38"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "hg38-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
        }
      },
      "geneticCodes": {
        "chrM": 2
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "ncbi_refseq_genes",
      "name": "NCBI RefSeq genes",
      "assemblyNames": ["hg38"],
      "category": ["Genes"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hela_rnaser_backsplice",
      "name": "HeLa RNase R+ back-splice junctions (STAR chimeric)",
      "assemblyNames": ["hg38"],
      "category": ["circRNA"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "https://jbrowse.org/demos/circrna/SRR1636985.backsplice.bed.gz"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "displayId": "hela_rnaser_backsplice-LinearMarkDisplay",
          "marks": [
            {
              "mark": "link",
              "encoding": {
                "strokeWidth": {
                  "field": "score",
                  "scale": { "type": "log", "range": [1, 8] }
                }
              }
            },
            {
              "mark": "text",
              "encoding": { "text": "score" },
              "maxBpPerPx": 50
            }
          ]
        }
      ]
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "hela_rnaser_reads",
      "name": "HeLa RNase R+ RNA-seq (SRR1636985)",
      "assemblyNames": ["hg38"],
      "category": ["circRNA"],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://jbrowse.org/demos/circrna/SRR1636985.slice.bam"
      },
      "displayDefaults": {
        "height": 300,
        "sashimi": { "labels": { "show": true } },
        "filter": [{ "field": "mapq", "gte": 1 }]
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "hela_control_reads",
      "name": "HeLa ribominus RNA-seq, no RNase R (SRR1637089)",
      "assemblyNames": ["hg38"],
      "category": ["circRNA"],
      "adapter": {
        "type": "BamAdapter",
        "uri": "https://jbrowse.org/demos/circrna/SRR1637089.slice.bam"
      },
      "displayDefaults": {
        "height": 300,
        "sashimi": { "labels": { "show": true } },
        "filter": [{ "field": "mapq", "gte": 1 }]
      }
    }
  ],
  "defaultSession": {
    "name": "circHIPK3",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "hg38",
        "loc": "chr11:33,284,000-33,290,000",
        "tracks": [
          "ncbi_refseq_genes",
          "hela_rnaser_backsplice",
          "hela_rnaser_reads",
          "hela_control_reads"
        ]
      }
    ]
  }
}