Working with Illumina Basecalling and Demultiplexing input and output files


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Documentation for package ‘basecallQC’ version 1.30.0

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baseCallMetrics Gather basecalling metrics from a Run (using Run's ConversionStats.xml file).
basecallQC The basecallQC object and constructor.
basecallQC-basecallQC The basecallQC object and constructor.
basecallQC-class The basecallQC object and constructor.
BCL2FastQparams The Parameters for BCL2FastQparams object.
BCL2FastQparams-BCL2FastQparams The Parameters for BCL2FastQparams object.
BCL2FastQparams-class The Parameters for BCL2FastQparams object.
createBasemasks Function to create basemasks for basecalling from Illumina samplesheet (for bcl2Fastq versions >= 2.1.7).
createBCLcommand Function to create command for Illumina basecalling/demultiplexing using bcl2fastq versions >= 2.1.7.
demultiplexMetrics Gather demultiplexing metrics from a Run (using Run's DemultiplexingStats.xml file).
demuxBarplot Barplot of Illumina demultiplexing statistics.
demuxBarplot-method Barplot of Illumina demultiplexing statistics.
demuxBarplot.basecallQC Barplot of Illumina demultiplexing statistics.
demuxBoxplot Boxplot of Illumina demultiplexing statistics.
demuxBoxplot-method Boxplot of Illumina demultiplexing statistics.
demuxBoxplot.basecallQC Boxplot of Illumina demultiplexing statistics.
indexlengths Index lengths
indexlengths,BCL2FastQparams-method, Index lengths
indexlengths-method Index lengths
indexlengths.bcl2fastqparams Index lengths
interOpsReport Function to parse InterOps files and generate summary reports
makeFQTable Generate an HTML table linking to per sample summary fastq QC statistics from ShortRead
passFilterBar Barplot of Illumina basecalling statistics for reads passing filter.
passFilterBar-method Barplot of Illumina basecalling statistics for reads passing filter.
passFilterBar.basecallQC Barplot of Illumina basecalling statistics for reads passing filter.
passFilterBoxplot Boxplot of Illumina basecalling statistics for reads passing filter.
passFilterBoxplot-method Boxplot of Illumina basecalling statistics for reads passing filter.
passFilterBoxplot.basecallQC Boxplot of Illumina basecalling statistics for reads passing filter.
passFilterTilePlot Tile plot of Illumina basecalling statistics for reads passing filter.
passFilterTilePlot-method Tile plot of Illumina basecalling statistics for reads passing filter.
passFilterTilePlot.basecallQC Tile plot of Illumina basecalling statistics for reads passing filter.
readlengths Read lengths
readlengths,BCL2FastQparams-method, Read lengths
readlengths-method Read lengths
readlengths.bcl2fastqparams Read lengths
reportBCL Generate basecallQC report
reportBCL-method Generate basecallQC report
reportBCL.basecallQC Generate basecallQC report
summaryConvStatsTable Creates an HTML table of per sample summary statistics from basecalling results
summaryConvStatsTable-method Creates an HTML table of per sample summary statistics from basecalling results
summaryConvStatsTable.basecallQC Creates an HTML table of per sample summary statistics from basecalling results
summaryDemuxTable Generate an HTML table of per sample summary demultiplexing statistics
summaryDemuxTable-method Generate an HTML table of per sample summary demultiplexing statistics
summaryDemuxTable.basecallQC Generate an HTML table of per sample summary demultiplexing statistics
validateBCLSheet Illumina sample sheet cleaning and updating for bcl2Fastq versions >= 2.1.7