Assessment of duplication rates in RNA-Seq datasets
meta:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end
bam:file
BAM/SAM file containing read alignments
*.{bam}
meta2:map
Groovy Map containing reference information e.g. [ id:‘human’ ]
gtf:file
Genomic features annotation in GTF or SAF
*.{gtf}
scatter2d
Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]
[ id:'sample1', single_end:false ]
*_duprateExpDens.pdf:file
PDF duplication rate against total read count plot
*_duprateExpDens.pdf
boxplot
*_duprateExpBoxplot.pdf:file
PDF duplication rate ~ total reads per kilobase (RPK) boxplot
*_duprateExpBoxplot.pdf
hist
*_expressionHist.pdf:file
PDF expression histogram
*.pdf
dupmatrix
*_dupMatrix.txt:file
Text file containing tags falling on the features described in the GTF file
*_dupMatrix.txt
intercept_slope
*_intercept_slope.txt:file
Text file containing intercept and slope from dupRadar modelling
*_intercept_slope.txt
multiqc
*_mqc.txt:file
dupRadar files for passing to MultiQC
*_multiqc.txt
session_info
*.R_sessionInfo.log:file
dump of R SessionInfo
*.log
versions
versions.yml:file
File containing software versions
versions.yml
