starChipIndex: Preparing the bed file required by starchip to detect...

In kendomaniac/docker4seq: Running NGS computing demanding applications, e.g reads mapping and counting, wrapped in docker containers

Preparing the bed file required by starchip to detect circular RNAs on paired-end sequences

Description

This function prepare the genome bed file for starchip, the GTF must be the one used by starChimeric

Usage

starChipIndex(group = c("sudo", "docker"), genome.folder = getwd())

Arguments

group	a character string. Two options: sudo or docker, depending to which group the user belongs
genome.folder	a character string indicating the folder where the indexed reference genome for STAR is located.

Value

the bed files of the reference genome for STARChip analysis

Author(s)

Raffaele Calogero, raffaele.calogero [at] unito [dot] it, Bioinformatics and Genomics unit, University of Torino Italy

Examples

## Not run: 
    starChipIndex(group="docker", genome.folder="/data/genomes/hg38star")

## End(Not run)

kendomaniac/docker4seq documentation built on Sept. 3, 2024, 6:42 p.m.