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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 |
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cd $SCRATCH/byteclub/multiqc/01_fastq
multiqc . |
When this completes you'll see a new file and directory:
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To view the file you created in a web browser, it must be copied somwhere where a browser can open it. An easy way to do this is to copy it to your laptop like this, for example, changing the user name from abattenh and scratch path as appropriate. | Code Block |
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| # from your laptop:
scp -p abattenh@ls5.tacc.utexas.edu:/scratch/01063/abattenh/byteclub/multiqc/01_fastq/multiqc_report.html . |
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Add a few customizations
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Use your favorite text editor to create a a file called multiqc_config.yaml in your $SCRATCH/byteclub/multiqc/01_fastq directory as shown below. This will add report title lines and change the names of the MultiQC output files.
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To catch up, just stage Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc/
cd $SCRATCH/byteclub/multiqc/
rsync -avrP --delete /work/01063/abattenh/projects/byteclub/multiqc/01_fastq/ 01_fastq/. |
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After saving this file, remove the previous MultiQC outputs and re-run the program:
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cd $SCRATCH/byteclub/multiqc/01_fastq
rm -rf multiqc_data multiqc_report.html
multiqc . |
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First stage some mm10 bowtie2 alignment data:
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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/ |
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MultiQC will look at all files in this directory looking for report formats it understands. Here, reports that MultiQC will recognize as-is include:
- <prefix>.flagstat.txt - output from running samtools flagstat
- <prefix>.idxstats.txt - output from running samtools idxstats
- <prefix>.dupinfo.txt - output from running Picard MarkDuplicates
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!
Get ready to re-run MultiQC using the 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 . |
- <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: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc/
cd $SCRATCH/byteclub/multiqc/
rsync -avrP --delete /work/01063/abattenh/projects/byteclub/multiqc/03_bowtie/ 02_bowtie/. |
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Now run multiqc again:
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cd $SCRATCH/byteclub/multiqc/02_bowtie
rm -rf mqc_report*
multiqc . |
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mkdir -p $SCRATCH/byteclub/multiqc/02_bowtie/for_multiqc
cd $SCRATCH/byteclub/multiqc/02_bowtie/for_multiqc
for f in ../bowtie2/*.dupinfo.txt; do
bn=`basename $f`
pfx=${bn%%.dupinfo.txt}
echo "$f - $pfx"
cat $f | sed 's/[.]sort//g' > ${pfx}.dupmetrics.txt
done |
Your $SCRATCH/byteclub/multiqc/02_bowtie/for_multiqc directory should have 2 files:
- brain_50k_nuclei.fixed.dupmetrics.txt
- brain_50k_nuclei.fixed.dupmetrics.txt
The final piece of the puzzle is to tell MultiQC to ignore the original <prefix>.dupinfo.txt files by modifying the multiqc_config.yaml file, adding a fn_ignore_files list entry.
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063/abattenh/projects/byteclub/multiqc/04_picard_fixed/ 02_bowtie/. |
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After making this config file modification, you can now run multiqc again:
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cd $SCRATCH/byteclub/multiqc/02_bowtie; rm -rf mqc_report*; multiqc . |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063/abattenh/projects/byteclub/multiqc/05_section_order/ 02_bowtie/. |
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After making this config file modification, you can now run multiqc again:
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cd $SCRATCH/byteclub/multiqc/02_bowtie; rm -rf mqc_report*; multiqc . |
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cd $SCRATCH/byteclub/multiqc/02_bowtie/for_multiqc
for f in ../bowtie2/*.insertsz.txt; do
bn=`basename $f`
pfx=${bn%%.insertsz.txt}
echo "$f - $pfx"
tail -n +2 $f | grep -v -P '^-' | cut -f 1,3 > ${pfx}.bowtie2_isizes.tsv
done |
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cd $SCRATCH/byteclub/multiqc/02_bowtie
cp /work/01063/abattenh/projects/byteclub/multiqc/07_custom_bargraph/for_multiqc/*mapq* for_multiqc/
cp /work/01063/abattenh/projects/byteclub/multiqc/07_custom_bargraph/for_multiqc/*genomecov* for_multiqc/ |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP /work/01063/abattenh/projects/byteclub/multiqc/07_custom_bargraph/ 02_bowtie/. |
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Then the usual...
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cd $SCRATCH/byteclub/multiqc/02_bowtie; rm -rf mqc_report*; multiqc . |
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cd $SCRATCH/byteclub/multiqc/02_bowtie/for_fastqc
ln -s -f ../fastqc
cp -p ../bowtie2/*.flagstat.txt .
cp -p ../bowtie2/*.idxstats.txt . |
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brain_50k_nuclei.bowtie2_isizes.tsv
brain_50k_nuclei.dupmetrics.txt
brain_50k_nuclei.flagstat.txt
brain_50k_nuclei.idxstats.txt
brain_50k_nuclei.mapq_histogram.tsv
brain_5k_nuclei.bowtie2_isizes.tsv
brain_5k_nuclei.dupmetrics.txt
brain_5k_nuclei.flagstat.txt
brain_5k_nuclei.idxstats.txt
brain_5k_nuclei.mapq_histogram.tsv
combined_genomecov.tsv
fastqc |
Then:
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| language | bash |
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cd ~/playtime/multiqc/atacseq; rm -rf mqc_report*
multiqc for_multiqc |
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To catch up, just use Anna's pre-made files: | Code Block |
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| mkdir -p $SCRATCH/byteclub/multiqc
cd $SCRATCH/byteclub/multiqc
rsync -avrP --delete /work/01063/abattenh/projects/byteclub/multiqc/08_final/ 02_bowtie/. |
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Run MultiQC again, but this time just point it
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cd $SCRATCH/byteclub/multiqc/02_bowtie
rm -rf mqc_report*
multiqc for_multiqc |
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fn_ignore_dirs:
- 'bowtie2' |
In either case, the final report should look just as it did for the previous section: http://web.corral.tacc.utexas.edu/iyer/byteclub/multiqc/08_final.mqc_report.html.
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