rnaseq_de_sample

rnaseq_de.yml

rnaseq_de:
  workflow_id: 8cd7bdc8d3cf35cd
  workflow_target_type: stored_workflow
  request_state:
    Sample sheet of sequencing reads:
      class: Collection
      collection_type: sample_sheet:paired
      name: RNA-Seq DE sample sheet
      elements:
        - class: Collection
          collection_type: paired
          name: CRISPRi-C26-0.5-rep1
          elements:
          - class: File
            name: forward
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/094/SRR29244694/SRR29244694_1.fastq.gz"
            ext: "fastqsanger.gz"
          - class: File
            name: reverse
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/094/SRR29244694/SRR29244694_2.fastq.gz"
            ext: "fastqsanger.gz"
        - class: Collection
          collection_type: paired
          name: CRISPRi-dxr-0.5-rep1
          elements:
          - class: File
            name: forward
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/008/SRR29244608/SRR29244608_1.fastq.gz"
            ext: "fastqsanger.gz"
          - class: File
            name: reverse
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/008/SRR29244608/SRR29244608_2.fastq.gz"
            ext: "fastqsanger.gz"
        - class: Collection
          collection_type: paired
          name: CRISPRi-C26-0.5-rep2
          elements:
          - class: File
            name: forward
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/093/SRR29244693/SRR29244693_1.fastq.gz"
            ext: "fastqsanger.gz"
          - class: File
            name: reverse
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/093/SRR29244693/SRR29244693_2.fastq.gz"
            ext: "fastqsanger.gz"
        - class: Collection
          collection_type: paired
          name: CRISPRi-dxr-0.5-rep2
          elements:
          - class: File
            name: forward
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/007/SRR29244607/SRR29244607_1.fastq.gz"
            ext: "fastqsanger.gz"
          - class: File
            name: reverse
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/007/SRR29244607/SRR29244607_2.fastq.gz"
            ext: "fastqsanger.gz"
        - class: Collection
          collection_type: paired
          name: CRISPRi-C26-0.5-rep3
          elements:
          - class: File
            name: forward
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/092/SRR29244692/SRR29244692_1.fastq.gz"
            ext: "fastqsanger.gz"
          - class: File
            name: reverse
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/092/SRR29244692/SRR29244692_2.fastq.gz"
            ext: "fastqsanger.gz"
        - class: Collection
          collection_type: paired
          name: CRISPRi-dxr-0.5-rep3
          elements:
          - class: File
            name: forward
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/006/SRR29244606/SRR29244606_1.fastq.gz"
            ext: "fastqsanger.gz"
          - class: File
            name: reverse
            location: "ascp://fasp.sra.ebi.ac.uk/vol1/fastq/SRR292/006/SRR29244606/SRR29244606_2.fastq.gz"
            ext: "fastqsanger.gz"
      column_definitions:
      - type: string
        name: Condition
        optional: False
      - type: int
        name: Replicate
        optional: True
      - type: string
        name: Batch 1
        optional: True
      rows:
        CRISPRi-C26-0.5-rep1:
        - ctrlg
        - 1
        - "0.5"
        CRISPRi-dxr-0.5-rep1:
        - dxr
        - 1
        - "0.5"
        CRISPRi-C26-0.5-rep2:
        - ctrlg
        - 2
        - "0.5"
        CRISPRi-dxr-0.5-rep2:
        - dxr
        - 2
        - "0.5"
        CRISPRi-C26-0.5-rep3:
        - ctrlg
        - 3
        - "0.5"
        CRISPRi-dxr-0.5-rep3:
        - dxr
        - 3
        - "0.5"
    GTF File of annotation:
      class: File
      url: https://hgdownload.soe.ucsc.edu/hubs/GCF/045/689/255/GCF_045689255.1/genes/GCF_045689255.1_ASM4568925v1.ncbiGene.gtf.gz
      ext: gtf.gz
    Reference genome: GCF_045689255.1
    DESeq2 Design Formula: "~ Replicate + Condition"
    Generate additional QC reports: true
    Use featurecounts for generating count tables: true