niekwit/RNA-Seq

RNA-Seq pipeline

RNA-Seq pipeline

Software dependencies:

• FastQC
• MultiQC
• Trim Galore
• Salmon
• Python
  • PyYAML
• R
  • tximport
  • readr
  • GenomicFeatures
  • biomaRt
  • DESeq2

Installation:

In the command line, navigate to a directory where you want to install the scripts and run:

git clone https://github.com/niekwit/RNA-Seq.git

rna-seq.py can be permamently added to $PATH by adding the following line to ~/.bashrc:

export PATH=/path/to/RNA-Seq:$PATH

Configuration:

Usage:

usage: rna-seq.py [-h] [-t <int>] [-r {gencode-v35}] [-a {salmon,hisat2}] [-g]

optional arguments:
  -h, --help            show this help message and exit
  -t <int>, --threads <int>
                        Number of CPU threads to use (default is 1). Use max
                        to apply all available CPU threads. For Salmon 8-12
                        threads are optimal
  -r {gencode-v35}, --reference {gencode-v35}
                        Reference genome
  -a {salmon,hisat2}, --align {salmon,hisat2}
                        Choose aligner. Default is Salmon.
  -g, --go              GO analysis with DAVID

Output: