Installation¶
Software requirements¶
Required: Python 3 (pandas, numpy), R
TERA detect (TE identification): SERVE (v1.0), StringTie (v2.1.1), Telescope (v1.0.3)
TERA anno (TE annotation): BEDTools (v2.27.1)
TERA quant (TE quantification): Telescope (v1.0.3), RSEM (v1.2.28) or Kallisto (0.44.0)
Install via conda¶
conda env create -n tera -f environment.yml
conda activate tera
conda install -c bioconda gffread=0.12.1 stringtie bedtools
Install via singularity¶
singularity build TERA.sif TERA.def
Obtain TERA¶
git clone https://github.com/janky-yz/TERA.git
chmod u+x TERA/script/TERA