Basecalling and Demultiplexing Summary Report"

In basecallQC: Working with Illumina Basecalling and Demultiplexing input and output files

knitr::opts_chunk$set(echo = TRUE)

basecallQC Summary Report

The basecallQC summary report contains summary metrics on demultiplexing and basecalling for an Illumina Run.

Conversion Metrics

The yield of all samples before and after passing filter are presented in the table below.

summaryConvStatsTable(BCLQCreport,output="html")

The bar plot shown below illustrates the total Yield of samples before and after passing filter.

passFilterBar(BCLQCreport,groupBy = "Sample",
              metricToPlot = "Yield")+theme_bw()

The boxplot shows the distribution of Yield of samples before and after passing filter.

passFilterBoxplot(BCLQCreport,groupBy = "Sample",
              metricToPlot = "Yield")+theme_bw()

The below plot shows the Yield per Tile/Lane for the Illumina Run to allow for the identification of potentially problematic Tiles per lane.

passFilterTilePlot(BCLQCreport,
              metricToPlot = "Yield")

Demultiplexing Metrics

The demultiplexing count for all samples are shown in the below table.

summaryDemuxTable(BCLQCreport,output="html")

The below bar plot shows the results per sample for demultiplexing of the Run and so should help visually identify any samples which are less represented than expected.

demuxBarplot(BCLQCreport,groupBy = "Sample")+theme_bw()

if(doFQQC==TRUE){
  makeFQTable(BCLQCreport)
}

sessionInfo()

basecallQC documentation built on Nov. 8, 2020, 8:03 p.m.