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• Always use spaces (not tabs!) in the multiqc_config.yaml file.
• Make sure the file is saved with Unix line endings (not Windows or Mac).
• Pay attention to the output when running multiqc. It will tell you if there are issues parsing the config file.
• Always delete any previous MultiQC output files before running multiqc
  • While their documentation says existing files will just be updated, I have seen MultiQC get confused when previous reports exist.
• It is a good idea to change the name of the MultiQC output files
  • If output files with those names are not created, something went wrong!
• Consult example config files
  • An example multiqc_config.yaml file: https://github.com/ewels/MultiQC/blob/master/multiqc_config_example.yaml
  • All multiqc_config.yaml defaults: https://github.com/ewels/MultiQC/blob/master/multiqc/utils/config_defaults.yaml
• Avoid running multiqc on large complex directory trees.
  • Instead, create a separate directory (or directory tree) only for MultiQC 
    • Copy or link the files you want MultiQC to look for there, and use it as MultiQC's target directory.
  • MultiQC will run much faster and have fewer confusions.

Add reports from a bowtie2 alignment

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So a bit of command line reformatting is needed to produce files for MultiQC, which we will save in our for_multiqc directory.

mkdir -p ~/playtimecd $SCRATCH/byteclub/multiqc/atacseq02_bowtie/for_multiqc
for cd ~/playtime/multiqc/atacseq/for_multiqc
for f in f in ../bowtie2/*.insertsz.txt; do
  bn=`basename $f`
  pfx=${bn%%.insertsz.txt}
  echo "$f - $pfx"
  tail -n +2 $f | grep -v -P '^-' | cut -f 1,3 > ${pfx}.bowtie2_isizes.tsv
done

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Then the usual...

cd ~$SCRATCH/playtimebyteclub/multiqc/atacseq02_bowtie; rm -rf mqc_report*; multiqc .

Resulting in a report that includes our inset size distribution data the custom data section we configured: xxx. http:ftp://gapdhweb.corral.icmbtacc.utexas.edu/misciyer/byteclub/multiqc/06_custom_linegraph.mqc_report.custom_linegraph.htmlhtml, with a new section called Bowtie2 insert size.

What's cool is that this "sawtooth" insert size distribution occurs because of the way transposons insert into the major groove of DNA at regular intervals. So this graph shows Igor that his ATAC-seq proof-of-concept experiment worked!

References

Main MultiQC links

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