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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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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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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 |
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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
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To catch up, just use Anna's pre-made files:
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Next we edit the multiqc_config.yaml configuration file to add appropriate custom data sections:x
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# 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'
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To catch up, just use Anna's pre-made files:
To catch up, just use Anna's pre-made files:
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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.)
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countsample 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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