alignBowtie: aligns reads using bowtie

In dphansti/mango: ChIA-PET data analysis software

Description

This function aligns reads using bowtie

Usage

alignBowtie(fastq, output, bowtiepath, bowtieref, shortreads, threads,
  verbose = TRUE, nlines = 10000)

Arguments

fastq	full path to fastq file
bowtiepath	full path to bowtie
bowtieref	full path to bowtie reference
threads	the number of threads to be used for bowtie alignment
verbose	boolean whether or not to print command
nlines	the number of lines to look at to determine the scoring method
arguments	arguments to give to bowtie

dphansti/mango documentation built on May 15, 2019, 1:46 p.m.