This repository stores all the Python, R and shell files that are used to perform NGS analysis.

On the RNA-Seq folder, you will find the necessary tools to run a RNA-Seq pipeline on your terminal in a Unix environment. Several folder are located within it:

• data: fasta, gff and a subfolder subdata must be added in this folder.

  • subdata: fastq files are included in this folder.

• scripts: all the scripts needed to run the RNA-Seq analysis are found here.

A folder bin must be created where all the results will be stored. The user must follow the following steps before running the analysis

git clone https://github.com/jumagari14/Tabacum_Galaxy.git
cd Tabacum_Galaxy
tar xvzf RNA-Seq.tar.gz 
cd RNA-Seq
mkdir -p -m 755 bin data
mkdir -p -m 755 data/subdata
## Include all the necessary data in data and subdata folder
cd scripts 

Once these steps are done, a shell file can be executed

./improved_rna_seq.sh 

After running the pipeline, several folders are found in bin:

• genome_ind: Genome indexes, necessary to run the STAR mapping.
• STAR_Align: Sorted and unsorted Bam files from STAR mapping.
• counts: txt files with the counting results.
• trimm_data: trimmed fastq reads. A subfolder quality where html and zip files as a result of FASTQC analysis are stored is also generated.

In the main directory, a file .tabular where all the counting results are saved is created. This file will mainly be used in the latter normalisation step.