MultiQC logo

BISCUIT

Supported Tool

Maps bisulfite converted DNA sequence reads and determines cytosine methylation states

The module parses logs generated by BISCUIT and the quality control script, QC.sh, included with the BISCUIT software.

Note: As of MultiQC v1.9, the module supports only BISCUIT version v0.3.16 and onwards. If you have BISCUIT data from before this, please use MultiQC v1.8.

Insert Size Distribution

The second tab of this plot uses the config option read_count_multiplier, so if millions of reads is not useful for your data you can customise this.

See Number base (multiplier) in the documentation.

File search patterns

biscuit/align_isize:
  contents: BISCUITqc Insert Size Table
  fn: "*_isize_table.txt"
  num_lines: 3
biscuit/align_mapq:
  contents: BISCUITqc Mapping Quality Table
  fn: "*_mapq_table.txt"
  num_lines: 3
biscuit/align_strand:
  contents: BISCUITqc Strand Table
  fn: "*_strand_table.txt"
  num_lines: 3
biscuit/base_avg_retention_rate:
  fn: "*_totalBaseConversionRate.txt"
biscuit/covdist_all_base:
  fn: "*_covdist_all_base_table.txt"
biscuit/covdist_all_base_botgc:
  fn: "*_covdist_all_base_botgc_table.txt"
biscuit/covdist_all_base_topgc:
  fn: "*_covdist_all_base_topgc_table.txt"
biscuit/covdist_all_cpg:
  fn: "*_covdist_all_cpg_table.txt"
biscuit/covdist_all_cpg_botgc:
  fn: "*_covdist_all_cpg_botgc_table.txt"
biscuit/covdist_all_cpg_topgc:
  fn: "*_covdist_all_cpg_topgc_table.txt"
biscuit/covdist_q40_base:
  fn: "*_covdist_q40_base_table.txt"
biscuit/covdist_q40_base_botgc:
  fn: "*_covdist_q40_base_botgc_table.txt"
biscuit/covdist_q40_base_topgc:
  fn: "*_covdist_q40_base_topgc_table.txt"
biscuit/covdist_q40_cpg:
  fn: "*_covdist_q40_cpg_table.txt"
biscuit/covdist_q40_cpg_botgc:
  fn: "*_covdist_q40_cpg_botgc_table.txt"
biscuit/covdist_q40_cpg_topgc:
  fn: "*_covdist_q40_cpg_topgc_table.txt"
biscuit/cpg_retention_readpos:
  fn: "*_CpGRetentionByReadPos.txt"
biscuit/cph_retention_readpos:
  fn: "*_CpHRetentionByReadPos.txt"
biscuit/dup_report:
  contents: BISCUITqc Read Duplication Table
  fn: "*_dup_report.txt"
  num_lines: 3
biscuit/qc_cv:
  contents: BISCUITqc Uniformity Table
  fn: "*_cv_table.txt"
  num_lines: 3
biscuit/read_avg_retention_rate:
  fn: "*_totalReadConversionRate.txt"
Back to all modules