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rna-seq-tophat
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RNA-seq pipeline with tophat2 + cufflinks + trimmomatic + fastqc
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rna-seq-tophat/defaults

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  1. {

  2.   "gtf": "oss://pgx-reference-data/reference/tophat2/annotation/gencode.v22.annotation.gtf",

  3.   "genome_directory":"oss://pgx-reference-data/reference/tophat2/genome/",

  4.   "idx_prefix":"tophat2",

  5.   "adapter": "oss://pgx-reference-data/reference/illumina_adapter/TruSeq3-PE.fa",

  6.   "fastqc_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastqc:v0.11.5",

  7.   "fastqc_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  8.   "trimmomatic_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/trimmomatic:v0.3.8",

  9.   "trimmomatic_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  10.   "tophat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/tophat:2.0.14_js",

  11.   "tophat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

  12.   "cufflinks_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/cufflinks:v2.2.1",

  13.   "cufflinks_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc"

  14. }