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BISCUIT

note

Maps bisulfite converted DNA sequence reads and determines cytosine methylation states.

https://github.com/huishenlab/biscuit

DOI: 10.1093/nar/gkae097

MIT License

The module parses logs generated by the BISCUIT quality control script, QC.sh, which wraps biscuit qc and biscuit qc_coverage and adds an extra metric of base-averaged cytosine retention. It will search for all files output from QC.sh, though the user may run biscuit qc or biscuit qc_coverage separately, if desired.

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'
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