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Byte Club, October 18 2017. Using MultiQC to produce consolidated QC Reports. Anna Battenhouse, CSSB & CCBB.

Overview

  • MultiQC is a tool for aggregating NGS QC reports.
    • It does not produce reports, just combines them for unified visualization.
  • MultiQC "knows" the report formats of many existing NGS tools: 
    • FastQC, cutadapt, bowtie2, tophat, STAR, kallisto, HISAT2, samtools, featureCounts, HTSeq, MACS2, Picard, GATK
    • … and more!
  • MultiQC can also be configured to display other data via two straightforward steps:
  1. format the data appropriately (e.g. tab-delimited text files)
  2. create appropriate custom data entries in a multiqc_config.yaml configuration file
  • MultiQC produces neat, interactive plots in an HTML file.
    • So it can be used as a basic plotting tool for many kinds of reports and data, not just those produced by NGS tools!

References

MultiQC configuration files

MultiQC custom data support

Example Reports from Anna

Below are descriptions of two projects I've assisted with lately using MultiQC to help pull together visualizations assessing experiment quality.

I recommend using Chrome to view MultiQC reports.

The HTML reports generated by MultQC rely heavily on JavaScript and other dynamic web content scripting tools, and not all browsers support them equally well.

  • These example MultiQC reports below were generated by running the multiqc binary on a command line.
  • After inspecting them locally (by just opening them as files in a web browser), they were copied to a web-accessible location to share with others.
    • Here, that location is Iyer Lab's web-accessible directory on corral 

Igor Ponomarev ATAC-seq data

ATAC-seq is a transposon-insertion sequencing method where an engineered, activate transposon inserts in accessible ("open") chromatin. It is considered to be a much simpler protocol to standard DNase-seq, and requires less starting material as well.

Igor Ponomarev's lab (in WCAAR) performed the ATAC-seq protocol on 5k and 50k cell nuclei from mouse brain.

Marcotte lab amplicon sequencing

The Marcotte lab is working on a deep mutational screening project of a human gene transformed into yeast as an amplicon on a plasmid. Here, the gene is MVK, a gene in the yeast cholesterol biosynthesis pathway. The hsMVK gene is amplified with an error-prone polymerase to produce point mutations. Both the native yeast gene and the human ortholog (with which it shares no sequence similarity) are under on/off promoter control. The idea is to compare the mutations that accumulate in the active hsMVK gene, after many growth cycles, with a background in which the hsMVK gene is present but not active (the yeast MVKis doing the work) to see which mutations are favored or disfavored. As part of this project, Riddhiman Garge produced 19 datasets.

 

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