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
References¶
QualiMap http://qualimap.bioinfo.cipf.es/doc_html/index.html