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

meta (map)

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

scatter2d (file)

PDF duplication rate against total read count plot

*_duprateExpDens.pdf

boxplot (file)

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

*_duprateExpBoxplot.pdf

hist (file)

PDF expression histogram

*.pdf

dupmatrix (file)

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

*_dupMatrix.txt

intercept_slope (file)

Text file containing intercept and slope from dupRadar modelling

*_intercept_slope.txt

multiqc (file)

dupRadar files for passing to MultiQC

*_multiqc.txt

session_info (file)

dump of R SessionInfo

*.log

versions (file)

File containing software versions

versions.yml
maintainer
Github user pinin4fjords
get in touch
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