Workflow Overview

Process workflow¶

TODO add images to show workflow

Pipeline Checks¶

• Input files are checked that they meet standard formatting; some file access is reviewed

• Processes include:

  • INPUT_CHECK:SAMPLESHEET_CHECK
  • INPUT_CHECK:CHECK_CONTRASTS

• Output directories include:

  • check_contrasts

Pre-alignment¶

• Adaptors are trimmed, if blacklists are included, filtering occurs

• Processes include:

  • CUTADAPT
  • FILTER_BLACKLIST:BWA_MEM
  • FILTER_BLACKLIST:SAMTOOLS_FILTERALIGNED
  • FILTER_BLACKLIST:PICARD_SAMTOFASTQ
  • FILTER_BLACKLIST:CUSTOM_COUNTFASTQ

• Output directories include:

  • cutadapt

Alignment¶

• Samples are aligned using BWA; alignment stats are generated; samples are sorted and filtered

• Processes include:

  • ALIGN_GENOME:BWA_MEM
  • ALIGN_GENOME:SAMTOOLS_FLAGSTAT_ALIGN
  • ALIGN_GENOME:FILTER_QUALITY
  • ALIGN_GENOME:SAMTOOLS_SORT
  • ALIGN_GENOME:SAMTOOLS_FLAGSTAT_FILTER

• Output directories include:

  • bwa_mem
  • samtools_flagstat_align
  • samtools_filteraligned
  • samtools_sort
  • samtools_flagstat_filter

Deduplicate¶

• Processes include:

  • DEDUPLICATE:MACS2_DEDUP
  • DEDUPLICATE:INDEX_SINGLE
  • DEDUPLICATE:PICARD_DEDUP
  • DEDUPLICATE:INDEX_PAIRED

• Output directories include:

Quality Control¶

• Processes include:

  • PPQT_PROCESS
  • QC:FASTQC_RAW
  • QC:FASTQC_TRIMMED
  • QC:FASTQ_SCREE
  • QC:PRESEQ
  • QC:HANDLE_PRESEQ_ERROR
  • QC:PARSE_PRESEQ_LOG
  • QC:QC_STATS
  • QC:QC_TABLE

Deeptools analysis¶

• Processes include:

  • QC:DEEPTOOLS:BAM_COVERAGE
  • QC:DEEPTOOLS:BIGWIG_SUM
  • QC:DEEPTOOLS:PLOT_CORRELATION
  • QC:DEEPTOOLS:PLOT_PCA
  • QC:DEEPTOOLS:NORMALIZE_INPUT
  • QC:DEEPTOOLS:BED_PROTEIN_CODING
  • QC:DEEPTOOLS:COMPUTE_MATRIX
  • QC:DEEPTOOLS:PLOT_HEATMAP
  • QC:DEEPTOOLS:PLOT_PROFILE
  • QC:DEEPTOOLS:PLOT_FINGERPRINT

Peak calling¶

• Processes include:

  • PHANTOM_PEAKS
  • CALL_PEAKS:CALC_GENOME_FRAC
  • CALL_PEAKS:BAM_TO_BED
  • CALL_PEAKS:MACS_BROAD
  • CALL_PEAKS:MACS_NARROW
  • CALL_PEAKS:SICER
  • CALL_PEAKS:CONVERT_SICER
  • CALL_PEAKS:GEM
  • CALL_PEAKS:FILTER_GEM
  • CALL_PEAKS:FRACTION_IN_PEAKS
  • CALL_PEAKS:CONCAT_FRIPS
  • CALL_PEAKS:PLOT_FRIP
  • CALL_PEAKS:GET_PEAK_META
  • CALL_PEAKS:CONCAT_PEAK_META
  • CALL_PEAKS:PLOT_PEAK_WIDTHS

Consensus Peaks¶

• Processes include:

  • CONSENSUS_PEAKS:CAT_CAT
  • CONSENSUS_PEAKS:SORT_BED
  • CONSENSUS_PEAKS:BEDTOOLS_MERGE
  • CONSENSUS_PEAKS:- CONSENSUS_PEAKS:_OUT

Annotate¶

• Processes include:

  • ANNOTATE:CHIPSEEKER_PEAKPLOT
  • ANNOTATE:CHIPSEEKER_ANNOTATE
  • ANNOTATE:CHIPSEEKER_PLOTLIST
  • ANNOTATE:HOMER_MOTIFS
  • ANNOTATE:MEME_AME

Differential Analysis¶

• If there are more than 2 replicates per group then diffbind is performed; otherwise manorm pairewise analysis is performed

• Processes include:

  • DIFF:DIFFBIND:PREP_DIFFBIND
  • DIFF:DIFFBIND:DIFFBIND_RMD
  • DIFF:MANORM:MANORM_PAIRWISE