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If all went well, you should now see a mqc_report.html file that looks like this: http://web.corral.tacc.utexas.edu/iyer/byteclub/multiqc/03_bowtie.mqc_report.html, with new sections for Picard and Samtools reports.
Fix the Picard MarkDuplicates sample name
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The resulting report should look like this: ftp://gapdh.icmb.utexas.edu/misc/multiqc/04.mqc_report.fixed_align_info.html, with a cleaned up General Statistics table.
Controlling report section order
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| Code Block | ||
|---|---|---|
| ||
# 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' |
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| Expand | |||||
|---|---|---|---|---|---|
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To catch up, just use Anna's pre-made files:
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After making this config file modification, you can now run multiqc again:
| Code Block | ||
|---|---|---|
| ||
cd $SCRATCH/byteclub/multiqc/02_bowtie; rm -rf mqc_report*; multiqc . |
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