Calculate read duplication rate
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
the alignment in bam format
*.{bam}
bai{:bash}
BAM index file
*.{bai}
seq_xls{:bash}
Read duplication rate determined from mapping position of read
*seq.DupRate.xls
*seq.DupRate.xls{:bash}
pos_xls{:bash}
*pos.DupRate.xls{:bash}
Read duplication rate determined from sequence of read
*pos.DupRate.xls
pdf{:bash}
*.pdf{:bash}
plot of duplication rate
*.pdf
rscript{:bash}
*.r{:bash}
script to reproduce the plot
*.R
versions_rseqc{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
rseqc{:bash}
The tool name
read_duplication.py --version | sed "s/read_duplication.py //"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
