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}
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{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
