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

Description Usage Arguments Value Author(s) Examples

View source: R/starChipIndex.R

Description

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

Usage

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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

three files: dedup_reads.bam, which is sorted and duplicates marked bam file, dedup_reads.bai, which is the index of the dedup_reads.bam, and dedup_reads.stats, which provides mapping statistics

Author(s)

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

Examples

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

## End(Not run)

kendomaniac/docker4seq documentation built on Nov. 18, 2018, 11:12 a.m.