Calculate inner distance between read pairs.
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}
bed{:bash}
a bed file for the reference gene model
*.{bed}
distance{:bash}
the inner distances
*.inner_distance.txt
*distance.txt{:bash}
freq{:bash}
*freq.txt{:bash}
frequencies of different insert sizes
*.inner_distance_freq.txt
mean{:bash}
*mean.txt{:bash}
mean/median values of inner distances
*.inner_distance_mean.txt
pdf{:bash}
*.pdf{:bash}
distribution plot of inner distances
*.inner_distance_plot.pdf
rscript{:bash}
*.r{:bash}
script to reproduce the plot
*.inner_distance_plot.R
versions_rseqc{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
rseqc{:bash}
The tool name
inner_distance.py --version | sed "s/inner_distance.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.
