Description

Calculate inner distance between read pairs.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

bam (file)

the alignment in bam format

*.{bam}

bed (file)

a bed file for the reference gene model

*.{bed}

Output

Name (Type)
Description
Pattern

distance (file)

the inner distances

*.inner_distance.txt

freq (file)

frequencies of different insert sizes

*.inner_distance_freq.txt

mean (file)

mean/median values of inner distances

*.inner_distance_mean.txt

pdf (file)

distribution plot of inner distances

*.inner_distance_plot.pdf

rscript (file)

script to reproduce the plot

*.inner_distance_plot.R

versions (file)

File containing software versions

versions.yml
included in
callingcards rnaseq
authors
Github user drpatelh Github user kevinmenden
get in touch
Ask a question on Slack Open an issue on GitHub

Tools

rseqc
GPL-3.0-or-later

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data.

http://rseqc.sourceforge.net 10.1093/bioinformatics/bts356