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| Code Block |
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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 |
| Expand |
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| Or you can just copy a config file |
To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc/01_fastq
cd $SCRATCH/byteclub/multiqc/01_fastq
ln -s -f /work/01063/abattenh/projects/byteclub/multiqc/fastqc
cp /work/01063/abattenh/projects/byteclub/multiqc/conf/02_simple_custom.yaml multiqc_config.yaml . |
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After saving this file, remove the previous MultiQC outputs and re-run the program:
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Note that output from samtools flagstat and samtools idxstats will only be recognized by MultiQC if the files names include the words flagstat and idxstats. Fortunately, Anna's script created files with those names!
Now run multiqc again Get ready to re-run MultiQC using the previous MultiQC configuration created above.
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mkdir -p $SCRATCH/byteclub/multiqc/02_bowtie
cd $SCRATCH/byteclub/multiqc/02_bowtie
cp ../01_fastq/multiqc_config.yaml .
rm |
| Expand |
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To catch up, just use Anna's pre-made files: | Code Block |
|---|
| mkdir -p $SCRATCH/byteclub/multiqc/02_bowtie
cd $SCRATCH/byteclub/multiqc/02_bowtie
ln -s -f /work/01063/abattenh/projects/byteclub/multiqc/fastqc
rsync -avrP /work/01063/abattenh/projects/byteclub/multiqc/bowtie2/ bowtie2/
cp /work/01063/abattenh/projects/byteclub/multiqc/conf/02_simple_custom.yaml multiqc_config.yaml . |
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Now run multiqc again:
| Code Block |
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cd $SCRATCH/byteclub/multiqc/02_bowtie
rm -rf mqc_report*
multiqc . |
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| Code Block |
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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'' |
x
| Expand |
|---|
| Or you can just copy |
To catch up, just use Anna's pre-made files: | Code Block |
|---|
| mkdir -p $SCRATCH/byteclub/multiqc/01_fastq
cd $SCRATCH/byteclub/multiqc/02_bowtie
ln -s -f /work/01063/abattenh/projects/byteclub/multiqc/fastqc
rsync -avrP /work/01063/abattenh/projects/byteclub/multiqc/bowtie2/ bowtie2/
cp /work/01063/abattenh/projects/byteclub/multiqc/conf/04_fix_dupinfo.yaml multiqc_config.yaml
mkdir for_multiqc
cp /work/01063/abattenh/projects/byteclub/multiqc/for_multiqc/brain*.dupmetrics.txt for_multiqc/ |
|
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| Code Block |
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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' |
x
| Expand |
|---|
|
To catch up, just use Anna's pre-made files: | Code Block |
|---|
| mkdir -p $SCRATCH/byteclub/multiqc/02_bowtie
cd $SCRATCH/byteclub/multiqc/02_bowtie
ln -s -f /work/01063/abattenh/projects/byteclub/multiqc/fastqc
rsync -avrP /work/01063/abattenh/projects/byteclub/multiqc/bowtie2/ bowtie2/
cp /work/01063/abattenh/projects/byteclub/multiqc/conf/05_section_order.yaml multiqc_config.yaml
mkdir for_multiqc
cp /work/01063/abattenh/projects/byteclub/multiqc/for_multiqc/brain*.dupmetrics.txt for_multiqc/ |
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