DifferentialInteractionAnalysis/params.example.yml at master · RNABioInfo/DifferentialInteractionAnalysis · GitHub

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out_dir: results
analysis_method: both
metadata_file: data/metadata.csv
# Exact feature GFF supplied to RNAnue; stable pair-background IDs are read here.
annotations_file: data/TU_details_merged_utr_plus_missing_refseq.gff
rnanue_results_dir: /Volumes/chris_ssd_2/external/hyderabad_synechocystis/results_dark
# Optional stage overrides. By default the pipeline discovers stage directories
# and complete_super_interaction_* files from rnanue_results_dir, preferring
# 05_postprocess when present.
# detect_dir: /path/to/03_detect
# analyze_dir: /path/to/04_analyze
# postprocess_dir: /path/to/05_postprocess
primary_contrast:
  case_role: treatment
  control_role: ligation_control
qc_roles:
  - no_ligation_control
normalization:
  sample_exposure: split_reads
  pair_background: true
  offset_pseudocount: 0.5
batch_correction:
  mode: auto
  columns:
    - batch
  on_confounded: fail
  visualization_remove_batch: true
count_handling:
  edgeR: numeric
  DESeq2: round
high_confidence:
  rnanue_padj_max: 0.1
annotation:
  enabled: true
  # Optional final annotation override. Omit to reuse annotations_file.
  target_annotations_overwrite: data/TU_details_merged_utr_plus_missing_refseq.gff
  feature_types:
    - gene
    - sRNA
    - tRNA
    - rRNA
    - ncRNA
    - transcript
    - TU
    - CDS
    - mobile_genetic_element
  ignore_feature_types:
    - region
    - sequence_feature
  match_attributes:
    - ID
    - Name
    - gene
    - locus_tag
    - Alias
    - Parent
  biotype_attributes:
    - gene_biotype
    - biotype
    - gbkey
    - type
  seqname_normalization: auto_strip_version
  strand_policy: both
  min_overlap_bp: 1
  target_ids:
    - ncr0700
    - psrR1
    - csiR1
    - gene856
    - gene857
    - gene2199
    - gene2962
  target_result_sets:
    - high_confidence
    - concordant_same_direction
    - edgeR_significant
    - DESeq2_significant
min_inter_contr: 10
min_n_samples_contr: 2
min_n_samples_greater_zero: 3
feature_ids: ncr0700,psrR1,csiR1,gene856,gene857,gene2199,gene2962
padj_thresh: 0.1