Browse the output directory
This is an interactive display of exactly what results you'll get as output from PEPATAC:
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:fa-folder-open-o: PEPATAC_tutorial_reports/
- :fa-file-code-o: cfrif.html
- :fa-file-code-o: fastqc_report_r1.html
- :fa-file-code-o: fastqc_report_r2.html
- :fa-file-code-o: fragment_distribution.html
- :fa-file-code-o: frif.html
- :fa-file-code-o: library_complexity.html
- :fa-file-code-o: objects.html
- :fa-file-code-o: peak_chromosome_distribution.html
- :fa-file-code-o: peak_partition_distribution.html
- :fa-file-code-o: samples.html
- :fa-file-code-o: status.html
- :fa-file-code-o: tss_distance_distribution.html
- :fa-file-code-o: tss_enrichment.html
- :fa-file-code-o: tutorial1.html
- :fa-file-code-o: tutorial2.html
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:fa-folder-open-o: results_pipeline/
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:fa-folder-open-o: tutorial1/
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:fa-folder-open-o: fastqc/
- :fa-file-code-o: tutorial1_R1_trim_fastqc.html
- :fa-file-archive-o: tutorial1_R1.trim_fastqc.zip
- :fa-file-code-o: tutorial1_R2_trim_fastqc.html
- :fa-file-archive-o: tutorial1_R2.trim_fastqc.zip
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:fa-folder-open-o: raw/
- :fa-file-archive-o: tutorial1_r1.fastq.gz
- :fa-file-archive-o: tutorial1_r2.fastq.gz
- :fa-file-archive-o: hg38_annotations.bed.gz
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:fa-folder-open-o: aligned_hg38/
- :fa-file-o: tutorial1_fail_qc.bam
- :fa-file-o: tutorial1_sort.bam
- :fa-file-o: tutorial1_sort.bam.bai
- :fa-file-o: tutorial1_unmap.bam
- :fa-file-text-o: tutorial1_dedup_metrics_log.txt
- :fa-file-o: tutorial1_sort_dedup.bam
- :fa-file-o: tutorial1_sort_dedup.bam.bai
- :fa-file-o: tutorial1_smooth.bw
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:fa-folder-open-o: aligned_hg38_exact/
- :fa-file-o: tutorial1_exact.bw
- :fa-file-o: tutorial1_shift.bed
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:fa-folder-open-o: fastq/
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:fa-folder-open-o: peak_calling_hg38/
- :fa-file-o: tutorial1_peaks.narrowPeak
- :fa-file-excel-o: tutorial_peaks.xls
- :fa-file-o: tutorial1_summits.bed
- :fa-file-o: tutorial1_peaks.bigBed
- :fa-file-o: tutorial1_peaks_coverage.bed
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:fa-folder-open-o: prealignments/
- :fa-file-text-o: tutorial1_rCRSd_bt_aln_summary.log
- :fa-file-archive-o: tutorial1_rCRSd_unmap_R1.fq.gz
- :fa-file-archive-o: tutorial1_rCRSd_unmap_R2.fq.gz
- :fa-file-text-o: tutorial1_human_repeats_bt_aln_summary.log
- :fa-file-archive-o: tutorial1_human_repeats_unmap_R1.fq.gz
- :fa-file-archive-o: tutorial1_human_repeats_unmap_R2.fq.gz
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:fa-folder-open-o: QC_hg38/
- :fa-file-o: tutorial1_bamQC.tsv
- :fa-file-pdf-o: tutorial1_cFRiF.pdf
- :fa-file-image-o: tutorial1_cFRiF.png
- :fa-file-pdf-o: tutorial1_peak_chromosome_distribution.pdf
- :fa-file-image-o: tutorial1_peak_chromosome_distribution.png
- :fa-file-text-o: tutorial1_fragCount.txt
- :fa-file-pdf-o: tutorial1_fragLenDistribution.pdf
- :fa-file-image-o: tutorial1_fragLenDistribution.png
- :fa-file-text-o: tutorial1_fragLenDistribution.txt
- :fa-file-text-o: tutorial1_fragLen.txt
- :fa-file-pdf-o: tutorial1_FRiF.pdf
- :fa-file-image-o: tutorial1_FRiF.png
- :fa-file-pdf-o: tutorial1_peak_genomic_distribution.pdf
- :fa-file-image-o: tutorial1_peak_genomic_distribution.png
- :fa-file-text-o: tutorial1_preseq_counts.txt
- :fa-file-text-o: tutorial1_preseq_out.txt
- :fa-file-pdf-o: tutorial1_preseq_plot.pdf
- :fa-file-image-o: tutorial1_preseq_plot.png
- :fa-file-text-o: tutorial1_preseq_yield.txt
- :fa-file-pdf-o: tutorial1_peak_TSS_distribution.pdf
- :fa-file-image-o: tutorial1_peak_TSS_distribution.png
- :fa-file-pdf-o: tutorial1_TSS_enrichment.pdf
- :fa-file-image-o: tutorial1_TSS_enrichment.png
- :fa-file-text-o: tutorial1_TssEnrichment.txt
- :fa-file-text-o: objects.tsv
- :fa-file-code-o: PEPATAC_cleanup.sh
- :fa-file-code-o: PEPATAC_commands.sh
- :fa-file-o: PEPATAC_completed.flag
- :fa-file-o: PEPATAC_log.md
- :fa-file-text-o: PEPATAC_profile.tsv
- :fa-file-text-o: stats.tsv
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:fa-folder-open-o: tutorial2/
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:fa-folder-open-o: fastqc/
- :fa-file-code-o: tutorial2_R1_trim_fastqc.html
- :fa-file-archive-o: tutorial2_R1.trim_fastqc.zip
- :fa-file-code-o: tutorial2_R2_trim_fastqc.html
- :fa-file-archive-o: tutorial2_R2.trim_fastqc.zip
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:fa-folder-open-o: raw/
- :fa-file-archive-o: tutorial2_r1.fastq.gz
- :fa-file-archive-o: tutorial2_r2.fastq.gz
- :fa-file-archive-o: hg38_annotations.bed.gz
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:fa-folder-open-o: aligned_hg38/
- :fa-file-o: tutorial2_fail_qc.bam
- :fa-file-o: tutorial2_sort.bam
- :fa-file-o: tutorial2_sort.bam.bai
- :fa-file-o: tutorial2_unmap.bam
- :fa-file-text-o: tutorial2_dedup_metrics_log.txt
- :fa-file-o: tutorial2_sort_dedup.bam
- :fa-file-o: tutorial2_sort_dedup.bam.bai
- :fa-file-o: tutorial2_smooth.bw
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:fa-folder-open-o: aligned_hg38_exact/
- :fa-file-o: tutorial2_exact.bw
- :fa-file-o: tutorial2_shift.bed
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:fa-folder-open-o: fastq/
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:fa-folder-open-o: peak_calling_hg38/
- :fa-file-o: tutorial2_peaks.narrowPeak
- :fa-file-excel-o: tutorial_peaks.xls
- :fa-file-o: tutorial2_summits.bed
- :fa-file-o: tutorial2_peaks.bigBed
- :fa-file-o: tutorial2_peaks_coverage.bed
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:fa-folder-open-o: prealignments/
- :fa-file-text-o: tutorial2_rCRSd_bt_aln_summary.log
- :fa-file-archive-o: tutorial2_rCRSd_unmap_R1.fq.gz
- :fa-file-archive-o: tutorial2_rCRSd_unmap_R2.fq.gz
- :fa-file-text-o: tutorial2_human_repeats_bt_aln_summary.log
- :fa-file-archive-o: tutorial2_human_repeats_unmap_R1.fq.gz
- :fa-file-archive-o: tutorial2_human_repeats_unmap_R2.fq.gz
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:fa-folder-open-o: QC_hg38/
- :fa-file-o: tutorial2_bamQC.tsv
- :fa-file-pdf-o: tutorial2_cFRiF.pdf
- :fa-file-image-o: tutorial2_cFRiF.png
- :fa-file-pdf-o: tutorial2_peak_chromosome_distribution.pdf
- :fa-file-image-o: tutorial2_peak_chromosome_distribution.png
- :fa-file-text-o: tutorial2_fragCount.txt
- :fa-file-pdf-o: tutorial2_fragLenDistribution.pdf
- :fa-file-image-o: tutorial2_fragLenDistribution.png
- :fa-file-text-o: tutorial2_fragLenDistribution.txt
- :fa-file-text-o: tutorial2_fragLen.txt
- :fa-file-pdf-o: tutorial2_FRiF.pdf
- :fa-file-image-o: tutorial2_FRiF.png
- :fa-file-pdf-o: tutorial2_peak_genomic_distribution.pdf
- :fa-file-image-o: tutorial2_peak_genomic_distribution.png
- :fa-file-text-o: tutorial2_preseq_out.txt
- :fa-file-pdf-o: tutorial2_peak_TSS_distribution.pdf
- :fa-file-image-o: tutorial2_peak_TSS_distribution.png
- :fa-file-pdf-o: tutorial2_TSS_enrichment.pdf
- :fa-file-image-o: tutorial2_TSS_enrichment.png
- :fa-file-text-o: tutorial2_TssEnrichment.txt
- :fa-file-text-o: objects.tsv
- :fa-file-code-o: PEPATAC_cleanup.sh
- :fa-file-code-o: PEPATAC_commands.sh
- :fa-file-o: PEPATAC_completed.flag
- :fa-file-o: PEPATAC_log.md
- :fa-file-text-o: PEPATAC_profile.tsv
- :fa-file-text-o: stats.tsv
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:fa-folder-open-o: submission/
- :fa-file-text-o: PEPATAC_summarizer_collate.log
- :fa-file-code-o: PEPATAC_summarizer_collate.sub
- :fa-file-text-o: PEPATAC_tutorial.log
- :fa-file-code-o: PEPATAC_tutorial.sub
- :fa-file-code-o: tutorial.yaml
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:fa-folder-open-o: summary/
- :fa-file-code-o: PEPATAC_collator_commands.sh
- :fa-file-text-o: PEPATAC_collator_completed.flag
- :fa-file-o: PEPATAC_collator_log.md
- :fa-file-text-o: PEPATAC_collator_profile.tsv
- :fa-file-pdf-o: PEPATAC_tutorial_alignmentPercent.pdf
- :fa-file-image-o: PEPATAC_tutorial_alignmentPercent.png
- :fa-file-pdf-o: PEPATAC_tutorial_alignmentRaw.pdf
- :fa-file-image-o: PEPATAC_tutorial_alignmentRaw.png
- :fa-file-pdf-o: PEPATAC_tutorial_libComplexity.pdf
- :fa-file-image-o: PEPATAC_tutorial_libComplexity.png
- :fa-file-image-o: PEPATAC_tutorial_hg38_peaks_coverage.png
- :fa-file-text-o: PEPATAC_tutorial_hg38_peaks_coverage.tsv
- :fa-file-image-o: PEPATAC_tutorial_hg38_consensusPeaks.png
- :fa-file-text-o: PEPATAC_tutorial_hg38_consensusPeaks.narrowPeak
- :fa-file-pdf-o: PEPATAC_tutorial_TSSEnrichment.pdf
- :fa-file-image-o: PEPATAC_tutorial_TSSEnrichment.png
- :fa-file-text-o: stats.tsv
- :fa-file-text-o: PEPATAC_tutorial_assets_summary.tsv
- :fa-file-text-o: PEPATAC_tutorial_objs_summary.tsv
- :fa-file-text-o: PEPATAC_tutorial_stats_summary.tsv
- :fa-file-code-o: PEPATAC_tutorial_summary.html