Description

Assessment of duplication rates in RNA-Seq datasets

Input

name:type
description
pattern

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}

Output

name:type
description
pattern

scatter2d

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_duprateExpDens.pdf:file

PDF duplication rate against total read count plot

*_duprateExpDens.pdf

boxplot

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_duprateExpBoxplot.pdf:file

PDF duplication rate ~ total reads per kilobase (RPK) boxplot

*_duprateExpBoxplot.pdf

hist

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_expressionHist.pdf:file

PDF expression histogram

*.pdf

dupmatrix

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_dupMatrix.txt:file

Text file containing tags falling on the features described in the GTF file

*_dupMatrix.txt

intercept_slope

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_intercept_slope.txt:file

Text file containing intercept and slope from dupRadar modelling

*_intercept_slope.txt

multiqc

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*_mqc.txt:file

dupRadar files for passing to MultiQC

*_multiqc.txt

session_info

meta:map

Groovy Map containing sample information e.g. [ id:'sample1', single_end:false ]

*.R_sessionInfo.log:file

dump of R SessionInfo

*.log

versions

versions.yml:file

File containing software versions

versions.yml