SalmonTE

What is SalmonTE?

SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data. It comes with Salmon which is a fast and accurate transcriptome quantification method. You can read the details of the pipeline and an example of real data study in our published paper in PSB 2018.

What I need to run SalmonTE? Why I have to use it?

• You only need to have a set of FASTQ files and phenotype data. Furthermore, SalmonTE automatically decided whether your dataset is paired-ends reads or not.
• conditions can be numeric or categorical. Based on the data type of the conditions of each sample, SalmonTE will run differential expression analysis or linear regression.
• Unlikely other TE analysis tools, SalmonTE gives you various visualized output.

Requirements & Installation

To use SalmonTE python and R must be installed before running it.

• Install python and R packages

For python:

Run following line in your console

pip3 install snakemake docopt pandas --user

For R: Run following lines in R console.

install.packages(c("tidyverse", "scales", "WriteXLS", "BiocManager"))
BiocManager::install("DESeq2", version = "3.8")

• Clone the repository

git clone https://github.com/hyunhwaj/SalmonTE

• Add PATH of SalmonTE to your .bashrc file:

export PATH=$PATH:/PATH_OF_SALMON_TE/

• Re log-in to terminal or use source command:

source ~/.bashrc