gentrap_example.json 1.43 KB
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{
  "samples" : {
    "sampleA" : {
      "libraries" : {
        "lib_1" : {
          "R1" : "/path/to/inputA_R1.fq.gz",
          "R2" : "/path/to/inputA_R2.fq.gz"
        }
      }
    },
    "sampleB" : {
      "libraries" : {
        "lib_1" : {
          "R1" : "/path/to/inputB_1_R1.fq.gz",
          "R2" : "/path/to/inputB_1_R2.fq.gz"
        },
        "lib_2": {
          "R1" : "/path/to/inputB_2_R1.fq.gz",
          "R2" : "/path/to/inputB_2_R2.fq.gz"
        }
      }
    }
  },
  "gentrap": {
    "output_dir": "/path/to/output_dir",
    "expression_measures": ["fragments_per_gene", "bases_per_gene", "bases_per_exon"],
    "strand_protocol": "non_specific",
    "aligner": "gsnap",
    "reference": "/share/isilon/system/local/Genomes-new-27-10-2011/H.Sapiens/hg19_nohap/gsnap/reference.fa",
    "annotation_gtf": "/path/to/data/annotation/ucsc_refseq.gtf",
    "annotation_bed": "/path/to/data/annotation/ucsc_refseq.bed",
    "annotation_refflat": "/path/to/data/annotation/ucsc_refseq.refFlat",
    "gsnap": {
      "dir": "/share/isilon/system/local/Genomes-new-27-10-2011/H.Sapiens/hg19_nohap/gsnap",
      "db": "hg19_nohap",
      "quiet_if_excessive": true,
      "npaths": 1
    },
    "cutadapt": {
      "minimum_length": 20
    },
    "mapping": {
      "flexiprep": {
        "fastqc": {
          "threads": 6,
          "nogroup": true
        }
      }
    },
    "rawbasecounter": {
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      "core_memory": "20G"
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    }
  }
}