output.md

ecSeq-DNAseq Output

This document describes the output produced by the pipeline.

Pipeline overview

The pipeline is built using Nextflow and processes data using the following steps:

• Read Trimming - read trimming with cutadapt
• Read Alignment - mapping trimmed reads with bowtie2
• Quality Control - generating FastQC and bamQC reports
• Pipeline Info - reports from nextflow about the pipeline run

Read Trimming

Input reads will be trimmed with cutadapt, and output to a new directory if specified by the user.

Output directory: ./trimming

Read Alignment

Depending on which options are specified to the pipeline, trimmed reads will be aligned with bowtie2.

Output directory: ./mapping

Quality Control

Following trimming, the pipeline will generate FastQC reports for each new set of reads. Following alignment, the pipeline will generate bamQC reports for each BAM file.

Output directory: ./trimming Output directory: ./mapping/<sample>

Pipeline Info

Nextflow has several built-in reporting tools that give information about the pipeline run.

Output directory: ./

• dag.svg
  • DAG graph giving a diagrammatic view of the pipeline run.
  • NB: If Graphviz was not installed when running the pipeline, this file will be in DOT format instead of SVG.
• report.html
  • Nextflow report describing parameters, computational resource usage and task bash commands used.
• timeline.html
  • A waterfall timeline plot showing the running times of the workflow tasks.
• trace.txt
  • A text file with machine-readable statistics about every task executed in the pipeline.