4. Expected Outputs¶

The following directories are created under the WORKDIR/results directory:

alignment_stats: this directory include information on the alignment of each sample
bam: this directory includes BAM files, statistics on samples, statistics on spike-in controls for each sample
bedgraph: this directory includes BEDGRAPH files and statistic summaries for each sample
bigwig: this directory includes the bigwig files for each sample
peaks: this directory contains a sub-directory that relates to the quality threshold used.
quality threshold
- contrasts: this directory includes the contrasts for each line listed in the contrast manifest
- peak_caller: this directory includes all peak calls from each peak_caller (SEACR, MACS2, GOPEAKS) for each sample
- annotation
  - go_enrichment: this directory includes gene set enrichment pathway predictions when run_go_enrichment is set to true in the config file.
  - homer: this directory includes the annotation output from HOMER
  - rose: this directory includes the annotation output from ROSE when run_rose is set to true in the config file.
qc: this directory includes MULTIQC reports and spike-in control reports (when applicable)

├── alignment_stats
├── bam
├── bedgraph
├── bigwig
├── fragments
├── peaks
│   ├── 0.05
│   │   ├── contrasts
│   │   │   ├── contrast_id1.dedup_status
│   │   │   └── contrast_id2.dedup_status
│   │   ├── gopeaks
│   │   │   ├── annotation
│   │   │   │   ├── go_enrichment
│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_tables
│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_html_report
│   │   │   │   ├── homer
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.gopeaks_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.gopeaks_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   └── rose
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.gopeaks_broad.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.gopeaks_narrow.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_broad.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.dedup.gopeaks_narrow.12500
│   │   │   └── peak_output
│   │   ├── macs2
│   │   │   ├── annotation
│   │   │   │   ├── go_enrichment
│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_tables
│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_html_report
│   │   │   │   ├── homer
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   └── rose
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.macs2_broad.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.macs2_narrow.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.macs2_broad.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.macs2_narrow.12500
│   │   │   └── peak_output
│   │   └── seacr
│   │   │   ├── annotation
│   │   │   │   ├── go_enrichment
│   │   │   │   │   ├── contrast_id1.dedup_status.go_enrichment_tables
│   │   │   │   │   └── contrast_id2.dedup_status.go_enrichment_html_report
│   │   │   │   ├── homer
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   │   ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.motifs
│   │   │   │   │   │   ├── homerResults
│   │   │   │   │   │   └── knownResults
│   │   │   │   └── rose
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_non_relaxed.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_non_stringent.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_relaxed.12500
│   │   │   │       ├── replicate_id1_vs_control_id.dedup_status.seacr_norm_stringent.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_non_relaxed.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_non_stringent.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_relaxed.12500
│   │   │   │       ├── replicate_id2_vs_control_id.dedup_status.seacr_norm_stringent.12500
│   │       └── peak_output
└── qc
    ├── fastqc_raw
    └── fqscreen_raw

Last update: 2024-07-16