compare detected splice junctions to reference gene model
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}
xls{:bash}
xls file with junction information
*.xls
*.xls{:bash}
rscript{:bash}
*.r{:bash}
Rscript to reproduce the plots
*.r
log{:bash}
*.log{:bash}
Log file of execution
*.junction_annotation.log
*.junction.bed{:bash}
bed file of annotated junctions
*.junction.bed
interact_bed{:bash}
*.Interact.bed{:bash}
Interact bed file
*.Interact.bed
pdf{:bash}
*junction.pdf{:bash}
junction plot
*.junction.pdf
events_pdf{:bash}
*events.pdf{:bash}
events plot
*.events.pdf
versions_rseqc{:bash}
${task.process}{:bash}
:string
The process the versions were collected from
rseqc{:bash}
The tool name
junction_annotation.py --version | sed "s/junction_annotation.py //"{:bash}
:eval
The expression to obtain the version of the tool
versions{:bash}
The expression to obtain the version of the tool of the tool
RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.
