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