(In development, don't install)

ezRNAseq: Analyze easily RNAseq data

System requirements

The following programs should be installed if you want to align RNAseq data using ezRNAseq:

GNU Parallel: GNU parallel is a shell tool for executing jobs in parallel using multiple cores in a computer or multiple computers.
STAR software for RNA sequencing data alignment
SAMtools: SAM Tools provide various utilities for manipulating alignments data in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Pandoc

required for the function ez_report()

https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md

cp -r /usr/lib/rstudio-server/bin/pandoc/ ~/bin/pandoc/
cp -r /usr/lib/rstudio-server/bin/pandoc/pandoc-citeproc ~/bin/pandoc/

Add this to your profile

export PATH=$PATH:~/bin/pandoc
export PATH=$PATH:~/bin/pandoc-citeproc

Download reference genome

Time ~40 min

library(ezRNAseq)
install_igenome("hg19", result_dir = "~/genomes")

Create STAR index

~ 45 min

fasta_file = "~/genomes/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa"
gtf_file = "~/genomes/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf"
starIndex_dir = "~/genomes/Homo_sapiens/UCSC/hg19/Sequence/StarIndex"

create_star_index(fasta_file, gtf_file, 
    thread = 25, starIndex_dir = starIndex_dir)

fasta_file and gtf_file are the path to fasta and gtf files respectively.

Mapping

Mapping to reference genome is done using STAR.
Required program: STAR & samtools
Required external data: reference genome

Outputs: