Generating Error Profiles(3)

Enhanced mapping statistics

We run:

qualimap bamqc

with the following parameters:

The complete commandline is:

qualimap bamqc -bam ~/workdir/mappings/basecall_tiny_porechopped_vs_wuhan.sorted.bam -nw 5000 -nt 14 -c -outdir ~/workdir/mappings/basecall_tiny_porechopped_vs_wuhan_qualimap/

and for Illumina:

qualimap bamqc -bam ~/workdir/mappings/illumina_vs_wuhan.sorted.bam -nw 5000 -nt 14 -c -outdir ~/workdir/mappings/illumina_vs_wuhan_qualimap/

You can view the results with firefox:

firefox ~/workdir/mappings/basecall_tiny_porechopped_vs_wuhan_qualimap/qualimapReport.html
or
firefox ~/workdir/mappings/illumina_vs_wuhan_qualimap/qualimapReport.html