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  • 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!

 


Tip

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.

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Code Block
languagebash
titlelonestar5 setup for multiqc
module load python
export PATH="/work/projects/BioITeam/ls5/binopt/multiqc-1.0:$PATH"
export PYTHONPATH="/work/projects/BioITeam/ls5/lib/python2.7/annab-packages:$PYTHONPATH"
 
# make sure it is working...
multiqc --help
Code Block
languagebash
titlestampede setup for multiqc
module load python
export PATH="/work/projects/BioITeam/stampede/binopt/multiqc-1.0:$PATH"
export PYTHONPATH="/work/projects/BioITeam/stampede/lib/python2.7/annab-packages:$PYTHONPATH"
 
# make sure it is working...
multiqc --help

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  • <prefix>.flagstat.txt - output from running samtools flagstat 
  • <prefix>.idxstats.txt - output from running samtools idxstats 
  • <prefix>.dupinfo.txt - output from running Picard MarkDuplicates  


Expand
titleCatch up

To catch up, just use Anna's pre-made files:

Code Block
languagebash
mkdir -p $SCRATCH/byteclub/multiqc/
cd $SCRATCH/byteclub/multiqc/
rsync -avrP --delete /work/projects/BioITeam/projects/byteclub/multiqc/03_bowtie/ .

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