chenqingwang
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RNAseq-alignment
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from fastq to bam files
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RNAseq-alignment/defaults

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  1. {   

  2.     "fastp_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/fastp:0.19.6",

  3.     "fastp_cluster": "OnDemand bcs.b2.3xlarge img-ubuntu-vpc",

  4.     "trim_front1": "0",

  5.     "trim_tail1": "0",

  6.     "max_len1": "0",

  7.     "trim_front2": "0",

  8.     "trim_tail2": "0",

  9.     "max_len2": "0",

  10.     "adapter_sequence": "AGATCGGAAGAGCACACGTCTGAACTCCAGTCA",

  11.     "adapter_sequence_r2": "AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT",

  12.     "disable_adapter_trimming": "0",

  13.     "length_required": "50",

  14.     "length_required1": "20",

  15.     "UMI": "0",

  16.     "umi_len": "0",

  17.     "umi_loc": "umi_loc",

  18.     "qualified_quality_phred": "20",

  19.     "disable_quality_filtering": "1",

  20.     "hisat2_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/hisat2:v2.1.0-2",

  21.     "hisat2_cluster": "OnDemand bcs.a2.3xlarge img-ubuntu-vpc",

  22.     "idx_prefix": "genome_snp_tran",

  23.     "idx": "oss://pgx-reference-data/reference/hisat2/grch38_snp_tran/",

  24.     "pen_cansplice":"0",

  25.     "pen_noncansplice":"3",

  26.     "pen_intronlen":"G,-8,1",

  27.     "min_intronlen":"30",

  28.     "max_intronlen":"500000",

  29.     "maxins":"500",

  30.     "minins":"0",

  31.     "samtools_docker": "registry.cn-shanghai.aliyuncs.com/pgx-docker-registry/samtools:v1.3.1",

  32.     "samtools_cluster": "OnDemand bcs.a2.large img-ubuntu-vpc",

  33.     "insert_size":"8000"

  34.     }