Parses the InterOps binary files produced by Illumina's Real Time Analysis sofware and used by Illumina's SAV sofware. InterOp binary files contain information on phasing/prephsing, yield,read numbers and basecalling quality score distributions per cycle. This interOpsReport functions parses and summarises the InterOps files, TileMetrics.bin and QMetrics.bin, and the Stats directory XML files, ConversionStats.xml and DemultiplexingStats.xml.
A BCL2FastQparams object.
TRUE or FALSE . TRUE reports progress through file parsing.
The interOpsReport function returns a list of machine and run information, basecalling quality information and demultiplexing information. The three named elements are descibed below.
"machineReport" A data.frame containing information machine and software parameters
"sequencingReport" A data.frame of mean cluster density, percentage clusters passing filter, phasing and prephasing percentages, number of reads total/passing filter and percent of reads with mean quality score > Q30 grouped by lane and read
"demuxReport" A data.frame of demultiplexing results containing yield, number of reads, percentage of reads with quality scores greater than >Q30 and the percent of total reads per lane. Results are summarised per lane for samples, underdetermined indexes and all indexes (identifed and unidentified).
A named list of length 3 containing machine and run information, basecalling quality information and demultiplexing information.
1 2 3 4 5 6
fileLocations <- system.file("extdata",package="basecallQC") runXML <- dir(fileLocations,pattern="runParameters.xml",full.names=TRUE) config <- dir(fileLocations,pattern="config.ini",full.names=TRUE) bcl2fastqparams <- BCL2FastQparams(runXML,config,runDir=getwd(),verbose=FALSE) # myRes_BCAGJ8ANXX <- interOpsReport(bcl2fastqparams,verbose=TRUE)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.