Oct 23, 2024

Public workspaceQuality Control

This protocol is a draft, published without a DOI.
  • Briley Park1
  • 1Dana Farber Cancer Institute
Briley Park
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Protocol Citation: Briley Park 2024. Quality Control. protocols.io https://protocols.io/view/quality-control-dqav5se6
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: In development
We are still developing and optimizing this protocol
Created: October 23, 2024
Last Modified: October 23, 2024
Protocol Integer ID: 110645
Abstract
quality control needed before continuing with the downstream analysis of any sequencing
Quality Control (FastQC, MultiQC)
Quality Control (FastQC, MultiQC)
FastQC gives a general quality metrics about raw fastq files. MultiQC collate pipeline QC from FastQC, TrimGalore, samtools flagstat, samtools idxstats, samtools stats, picard CollectMultipleMetrics, picard MarkDuplicates, Preseq, deepTools plotProfile, deepTools plotFingerprint, phantompeakqualtools and featureCounts.

#run fastqc on all fastq.gz files in directory and move all FastQC output files to the new directory
mkdir fastqc_results
fastqc *.fastq.gz
mv *.zip *.html fastqc_results/

#run mutliQC on fastQC files
multiqc fastqc_results/ -o multiqc_report