...
- basic FastQC report
- report on BWA mem alignments of the datasets to hsMVK amplicon and plasmid backbone contigs
- http://web.corral.tacc.utexas.edu/iyer/mvk/mvk_mqc_report.bwa.html
- standard reports from samtools flagstat, samtools idxstats, Picard MarkDuplicates
- custom data reports from bedtools genomecov and from insert size distribution data Anna computed
- report using custom data from a specialized deep mutational screening tool from the Jesse Bloom lab
- http://web.corral.tacc.utexas.edu/iyer/mvk/mvk_mqc_report.jbloom.html
- this tool looks only at the overlapping portions of paired-end R1 and R2 reads
Code Workshop
Setup to follow along
Login to ls5 at TACC.
| Code Block | ||
|---|---|---|
| ||
mkdir -p $SCRATCH/byteclub/multiqc |
| Code Block | ||
|---|---|---|
| ||
mkdir -p $SCRATCH/byteclub/multiqc |
Produce a consolidated FastQC report
...