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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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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!

Adding

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custom

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bargraphs

Here we'll create two custom bargraph reports, one for bowtie2 mapping qualities and a second showing genome coverage of the alignments.

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There is just one data file for genome coverage. Unlike the per-sample files, it has a header, with an arbitrary tag for the categories dataset names in the 1st column, then dataset followed by category names and their counts in subsequent columns. (I've re-formatted the data below for readability, but remember that all .tsv file data must be tab-separated.)

Code Block
titlecombined_genomecov.tsv
count sample    5k_nuclei   none 50k_nuclei
(a) none  2140984435   2175228345
(b) 1-2   237947623    351105871
(c) 3-10  308665107    186361275
(d) 11-50 38729079     17356704
(e) 51+   4545530         51+
5k_nuclei   2140984435  237947623  308665107  38729079  4545530
50k_nuclei  2175228345  351105871  186361275  17356704  819579

Here we edit the multiqc_config.yaml configuration file to add appropriate custom data sections:

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