Peak Calling Analysis

Output Description

This documentation describes the output we provide upon running the Nfcore/atacseq pipeline.

First of all, take a look at the Pipeline summary. It nicely describes which steps have been performed in which order.

WHILE YOU BROWSE THROUGH YOUR RESULTS, FOLLOW THIS NFCORE DOCUMENTATION..

It describes the output, and what can be found where. If you want to navigate your results and understand the folder structure, it is essential that you go through this documentation.

Quick start: Summary HTML reports

  • There are two summary reports to look at:
    • Location 1: bwa/mergedLibrary/ataqv/<PEAK_TYPE>/html/index.html
    • Location 2: multiqc/<PEAK_TYPE>/multiqc_report.html

Sample names

  • Location: samples*.csv
  • The Nfcore/atacseq pipeline automatically renames your samples. This renaming is based on a sample definition file we create, and concatenates the group label (first column) and the replicate number (second column).

Output data formats

  • To look at your data, these three file formats are most important:
    • bam: Mapping details of all reads (binary format)
    • bigwig: Normalized coverage tracks (binary format)
    • broadPeak/narrowPeak/bed: Peaks (broadPeak and narrowPeak are types of a bed format)