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4. Expected Outputs

The following directories are created under the output_directory, dependent on the Pass of the pipeline

First Pass (first_pass)

  • 01_trim: this directory includes trimmed FASTQ files
  • 02_assembled: this directory includes assembled FASTQ files
  • 03_aligned: this directory includes aligned BAM files and BED files
    • 01_bam: BAM files after alignment
    • 02_bed: converted bed files
    • 03_histograms: histograms of bed files

Second Pass (second_pass)

  • 04_dyads: this directory contains DYAD calculated files
    • 01_DYADs: this includes direct DYAD calculations
    • 02_histograms: this includes histogram occurances
    • 03_CSV: this includes the occurance data in CSV format

Third Pass (third_pass)

  • /path/to/output/contrast: this includes the contrast file for each sample provided in the contrasts.tsv manifest

All Passes

  • log: this includes log files
    • [date of run]: the slurm output files of the pipeline sorted by pipeline start time; copies of config and manifest files used in this specific pipeline run; error reporting script