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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!

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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

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  

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

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

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

# Titles to use for the report.
title: "ATAC-Seq QC Reports"
subtitle: null
intro_text: "MultiQC reports for Igor's ATAC-Seq proof-of-concept project."
report_header_info:
    - Sequenced by: 'GSAF'
    - Job: 'JA17277'
    - Run: 'SA17121'
    - Setup: '2x150'

# Change the output filenames
output_fn_name: mqc_report.html
data_dir_name: mqc_report_data

# Ignore these files / directories / paths when searching for reports
fn_ignore_files:
    - '*.dupinfo.txt'

# Modules that should come at the top of the report
top_modules:
    - 'generalstats'
    - 'fastqc'
    - 'samtools'
    - 'picard'

# --------------------------------
# Custom data
# --------------------------------

custom_data:
    bowtie2_isize:
        id: 'bowtie2_isize_section'
        section_name: 'Bowtie2 insert size'
        description: 'distribution for alignments (bowtie2 --local -X2000 --no-mixed --no-discordant)'
        file_format: 'tsv'
        plot_type: 'linegraph'
        pconfig:
            id: 'bowtie2_isize_plot'
            title: 'Insert sizes for proper pairs'
            xlab: 'Insert size'
            ylab: 'Count'
sp:
    bowtie2_isize_section:
        fn: '*.bowtie2_isizes.tsv'

mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/projects/BioITeam/projects/byteclub/multiqc/06_custom_linegraph/ .

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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.)

countsample     5k_nuclei none   50k_nuclei (a) none  2140984435   2175228345
(b) 1-2   237947623    351105871 (c) 3-10  308665107    186361275 (d) 11-50 38729079     51+
5k_nuclei   2140984435  237947623 17356704 (e)308665107 51+ 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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