RNA-seq

Scripts for RNA-seq, Windows subsystem on Linux

Getting Started

Requirement

1. Hardware

When STAR running, large size memory (~ 40GB in rat RNA-seq alinemnt) will be required.

2. Software

• pigz
  "A parallel implementation of gzip for modern multi-processor, multi-core machines"

• STAR
  "Spliced Transcripts Alignment to a Reference"
  https://github.com/alexdobin/STAR

• fastp
  "A tool designed to provide fast all-in-one preprocessing for FastQ files"
  https://github.com/OpenGene/fastp

• Subread
  "high-performance read alignment, quantification and mutation discovery"
  http://subread.sourceforge.net/

Installation

Check PATH to softwares

$ STAR --version
2.7.1a
$ fastp --version

$ featureCount --version
featureCounts v1.6.4

Pull repository

$ git clone https://github.com/hkrkizum/BashScript.git
...

if you do not have the analysistools described above, you can set up analysis environment using docker image.

$ docker pull hkrkizum/bioinfo_star:1.1
...
$ docker pull hkrkizum/bioinfo_fastp:1.1
...
$ docker pull hkrkizum/bioinfo_subread:1.0
...

Usage

auto_***.sh -i [full path of dir contain target files] -o [full path of output dir]