Browse the output directory

This is an interactive display of exactly what results you'll get as output from PEPATAC:

• PEPATAC_tutorial_reports/

  • cfrif.html
  • fastqc_report_r1.html
  • fastqc_report_r2.html
  • fragment_distribution.html
  • frif.html
  • library_complexity.html
  • objects.html
  • peak_chromosome_distribution.html
  • peak_partition_distribution.html
  • samples.html
  • status.html
  • tss_distance_distribution.html
  • tss_enrichment.html
  • tutorial1.html
  • tutorial2.html
• results_pipeline/

  • tutorial1/

    • fastqc/

      • tutorial1_R1_trim_fastqc.html
      • tutorial1_R1.trim_fastqc.zip
      • tutorial1_R2_trim_fastqc.html
      • tutorial1_R2.trim_fastqc.zip
    • raw/

      • tutorial1_r1.fastq.gz
      • tutorial1_r2.fastq.gz
      • hg38_annotations.bed.gz
    • aligned_hg38/

      • tutorial1_fail_qc.bam
      • tutorial1_sort.bam
      • tutorial1_sort.bam.bai
      • tutorial1_unmap.bam
      • tutorial1_dedup_metrics_log.txt
      • tutorial1_sort_dedup.bam
      • tutorial1_sort_dedup.bam.bai
      • tutorial1_smooth.bw
    • aligned_hg38_exact/

      • tutorial1_exact.bw
      • tutorial1_shift.bed
    • fastq/
    • peak_calling_hg38/

      • tutorial1_peaks.narrowPeak
      • tutorial_peaks.xls
      • tutorial1_summits.bed
      • tutorial1_peaks.bigBed
      • tutorial1_peaks_coverage.bed
    • prealignments/

      • tutorial1_rCRSd_bt_aln_summary.log
      • tutorial1_rCRSd_unmap_R1.fq.gz
      • tutorial1_rCRSd_unmap_R2.fq.gz
      • tutorial1_human_repeats_bt_aln_summary.log
      • tutorial1_human_repeats_unmap_R1.fq.gz
      • tutorial1_human_repeats_unmap_R2.fq.gz
    • QC_hg38/

      • tutorial1_bamQC.tsv
      • tutorial1_cFRiF.pdf
      • tutorial1_cFRiF.png
      • tutorial1_peak_chromosome_distribution.pdf
      • tutorial1_peak_chromosome_distribution.png
      • tutorial1_fragCount.txt
      • tutorial1_fragLenDistribution.pdf
      • tutorial1_fragLenDistribution.png
      • tutorial1_fragLenDistribution.txt
      • tutorial1_fragLen.txt
      • tutorial1_FRiF.pdf
      • tutorial1_FRiF.png
      • tutorial1_peak_genomic_distribution.pdf
      • tutorial1_peak_genomic_distribution.png
      • tutorial1_preseq_counts.txt
      • tutorial1_preseq_out.txt
      • tutorial1_preseq_plot.pdf
      • tutorial1_preseq_plot.png
      • tutorial1_preseq_yield.txt
      • tutorial1_peak_TSS_distribution.pdf
      • tutorial1_peak_TSS_distribution.png
      • tutorial1_TSS_enrichment.pdf
      • tutorial1_TSS_enrichment.png
      • tutorial1_TssEnrichment.txt
    • objects.tsv
    • PEPATAC_cleanup.sh
    • PEPATAC_commands.sh
    • PEPATAC_completed.flag
    • PEPATAC_log.md
    • PEPATAC_profile.tsv
    • stats.tsv
  • tutorial2/

    • fastqc/

      • tutorial2_R1_trim_fastqc.html
      • tutorial2_R1.trim_fastqc.zip
      • tutorial2_R2_trim_fastqc.html
      • tutorial2_R2.trim_fastqc.zip
    • raw/

      • tutorial2_r1.fastq.gz
      • tutorial2_r2.fastq.gz
      • hg38_annotations.bed.gz
    • aligned_hg38/

      • tutorial2_fail_qc.bam
      • tutorial2_sort.bam
      • tutorial2_sort.bam.bai
      • tutorial2_unmap.bam
      • tutorial2_dedup_metrics_log.txt
      • tutorial2_sort_dedup.bam
      • tutorial2_sort_dedup.bam.bai
      • tutorial2_smooth.bw
    • aligned_hg38_exact/

      • tutorial2_exact.bw
      • tutorial2_shift.bed
    • fastq/
    • peak_calling_hg38/

      • tutorial2_peaks.narrowPeak
      • tutorial_peaks.xls
      • tutorial2_summits.bed
      • tutorial2_peaks.bigBed
      • tutorial2_peaks_coverage.bed
    • prealignments/

      • tutorial2_rCRSd_bt_aln_summary.log
      • tutorial2_rCRSd_unmap_R1.fq.gz
      • tutorial2_rCRSd_unmap_R2.fq.gz
      • tutorial2_human_repeats_bt_aln_summary.log
      • tutorial2_human_repeats_unmap_R1.fq.gz
      • tutorial2_human_repeats_unmap_R2.fq.gz
    • QC_hg38/

      • tutorial2_bamQC.tsv
      • tutorial2_cFRiF.pdf
      • tutorial2_cFRiF.png
      • tutorial2_peak_chromosome_distribution.pdf
      • tutorial2_peak_chromosome_distribution.png
      • tutorial2_fragCount.txt
      • tutorial2_fragLenDistribution.pdf
      • tutorial2_fragLenDistribution.png
      • tutorial2_fragLenDistribution.txt
      • tutorial2_fragLen.txt
      • tutorial2_FRiF.pdf
      • tutorial2_FRiF.png
      • tutorial2_peak_genomic_distribution.pdf
      • tutorial2_peak_genomic_distribution.png
      • tutorial2_preseq_out.txt
      • tutorial2_peak_TSS_distribution.pdf
      • tutorial2_peak_TSS_distribution.png
      • tutorial2_TSS_enrichment.pdf
      • tutorial2_TSS_enrichment.png
      • tutorial2_TssEnrichment.txt
    • objects.tsv
    • PEPATAC_cleanup.sh
    • PEPATAC_commands.sh
    • PEPATAC_completed.flag
    • PEPATAC_log.md
    • PEPATAC_profile.tsv
    • stats.tsv
• submission/

  • PEPATAC_summarizer_collate.log
  • PEPATAC_summarizer_collate.sub
  • PEPATAC_tutorial.log
  • PEPATAC_tutorial.sub
  • tutorial.yaml
• summary/

  • PEPATAC_collator_commands.sh
  • PEPATAC_collator_completed.flag
  • PEPATAC_collator_log.md
  • PEPATAC_collator_profile.tsv
  • PEPATAC_tutorial_alignmentPercent.pdf
  • PEPATAC_tutorial_alignmentPercent.png
  • PEPATAC_tutorial_alignmentRaw.pdf
  • PEPATAC_tutorial_alignmentRaw.png
  • PEPATAC_tutorial_libComplexity.pdf
  • PEPATAC_tutorial_libComplexity.png
  • PEPATAC_tutorial_hg38_peaks_coverage.png
  • PEPATAC_tutorial_hg38_peaks_coverage.tsv
  • PEPATAC_tutorial_hg38_consensusPeaks.png
  • PEPATAC_tutorial_hg38_consensusPeaks.narrowPeak
  • PEPATAC_tutorial_TSSEnrichment.pdf
  • PEPATAC_tutorial_TSSEnrichment.png
  • stats.tsv
• PEPATAC_tutorial_assets_summary.tsv
• PEPATAC_tutorial_objs_summary.tsv
• PEPATAC_tutorial_stats_summary.tsv
• PEPATAC_tutorial_summary.html