Create a conda enviroment and install necessary dependecies
mamba env create -n reference_based_RNA-seq_analysis -f DE_analysis.yaml
Activate the conda enviroment
conda activate reference_based_RNA-seq_analysis
Running the master python script
./master_RNA_seq.py -p /path/to/directory/ -s 17NQ004_P1_R11,17NQ004_P2_R5 -r A,B,C -g TAIR10_chr_all.fas -a Araport11_GTF_genes_transposons.current.gtf -b TAIR10_GFF3_genes_transposons.gff -c config_DE.txt
The files used for the commands are in test_data.zip. The reference Arabidopsis genome, as well as the .gff and .gtf annotation must be downloaded from [https://www.arabidopsis.org/]