This pipeline takes some BAM files from ICGC and runs featureCounts on them.
This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline.
The pipeline is built using Nextflow and processes data using the following steps:
FastQC gives general quality metrics about your reads. It provides information about the quality score distribution across your reads, the per base sequence content (%T/A/G/C). You get information about adapter contamination and other overrepresented sequences.
For further reading and documentation see the FastQC help.
Output directory: results/fastqc
sample_fastqc.html- FastQC report, containing quality metrics for your untrimmed raw fastq files
zips/sample_fastqc.zip- zip file containing the FastQC report, tab-delimited data file and plot images
MultiQC is a visualisation tool that generates a single HTML report summarising all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in within the report data directory.
Output directory: results/multiqc
Project_multiqc_report.html- MultiQC report - a standalone HTML file that can be viewed in your web browser
Project_multiqc_data/- Directory containing parsed statistics from the different tools used in the pipeline
For more information about how to use MultiQC reports, see http://multiqc.info