...
- These example MultiQC reports below were generated by running the multiqc binary on a command line.
- After inspecting them locally (by just opening them as files in a web browser), they were copied to a web-accessible location to share with others.
Here, that location is Iyer Lab's web-accessible directory on corral
Igor Ponomarev ATAC-seq data
ATAC-seq is a transposon-insertion sequencing method where an engineered, activate transposon inserts in accessible ("open") chromatin. It is considered to be a much simpler protocol to standard DNase-seq, and requires less starting material as well.
Igor Ponomarev's lab (in WCAAR) performed the ATAC-seq protocol on 5k and 50k cell nuclei from mouse brain, producing 2 paired-end datasets.
- http://web.corral.tacc.utexas.edu/iyer/igor/mqc_report.html
- has both standard and custom data reports
Marcotte lab amplicon sequencing
The Marcotte lab is working on a deep mutational screening project of a human gene transformed into yeast as an amplicon on a plasmid. Here, the gene is MVK, a gene in the yeast cholesterol biosynthesis pathway. The hsMVK gene is amplified with an error-prone polymerase to produce point mutations. Both the native yeast gene and the human ortholog (with which it shares no sequence similarity) are under on/off promoter control. The idea is to compare the mutations that accumulate in the active hsMVK gene, after many growth cycles, with a background in which the hsMVK gene is present but not active (the yeast MVKis doing the work) to see which mutations are favored or disfavored. As part of this project, Riddhiman Garge produced 19 datasets.
- 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
How To
Produce a consolidated FastQC report