README.md

In pantastheo/RACEseqR: Downstream analysis R package for 5-RACE Next Generation Sequencing experiments

RACEseqR

A Next Generation Sequencing data analysis pipeline packed as an R package. The pipeline uses popular command line tools for the downstream analysis of a 5-RACE sequencig experiment.

Dependencies

The following programs and packages must be installed on your computer.

Package | Version -------------- | -------------- Cutadapt (optional)| >=1.12 Bowtie | 1.0.0 Samtools | >=1.3.1 Bedtools | >=2.17.0 Tmap (optional) | >=3.4.1

Installation

The best way to install RACEseqR is to use the install_github command from the devtools package.

library("devtools")
install_github("pantastheo/RACEseqR")
library("RACEseqR")

Usage

Either use RACEseqR to output graphs dirrectly to your workinf directory.

RACEseq(input_data, replicon_ref, mismatch = 0, RACE_adapter = NULL,
  str = NULL, end = NULL, filename, tmap = NULL)

Or use RACEseqR inside Rstudio to manually generate tables and graphs.

dataframe <- RACEseq(input_data, replicon_ref, mismatch = 0, RACE_adapter = NULL,
  str = NULL, end = NULL, filename, tmap = NULL)

Arguments

Arguments | Description -------------- | -------------- input_data | The input .fastq files to be used for the alignment. replicon_ref | The reference sequence to be used in the alignment. mismatch | The number of mismatches to be accepted during alignment. RACE_adapter | The RACE adapter to be trimmied using cutadapt . str | The start position of the binding region. end | The end position of the binding region. filename | The filename that will be used for the output pdf file. tmap | The option to use the Tmap aligner. Defaults NULL

pantastheo/RACEseqR documentation built on May 12, 2019, 6:16 p.m.