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,
SalmonTEautomatically 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,
SalmonTEwill run differential expression analysis or linear regression.
- Unlikely other TE analysis tools,
SalmonTEgives you various visualized output.
Requirements & Installation
R must be installed before running it.
Run following line in your console
pip3 install snakemake docopt pandas --user
R: Run following lines in
install.packages(c("tidyverse", "scales", "WriteXLS", "BiocManager")) BiocManager::install("DESeq2", version = "3.8")
- Clone the repository
git clone https://github.com/hyunhwaj/SalmonTE
PATHof SalmonTE to your
- Re log-in to terminal or use