Tandem Repeat Copy Number Variation in \n Expression Data

This repository contains pipelines to preprocess RNAseq .bam files for the analysis with TRAL.

Setup and Installation of Dependencies

Download this repository

git clone https://github.com/matteodelucchi/TR_CNV_in_expression_data.git

Set up the directory struture for the files and install all necessary programs by sourcing the respective file for installation in a local environment or a high-performance cluster environment

chmod 779 setup_environment_cluster.sh
./setup_environment_cluster.sh

Run Pipelines

The two proposed pipelines are provided in

reference-based_mapping_pipeline.sh
de-novo_assembly.sh

They are on early reasearch stage - don't run them as executables. Go through each line very carefully step by step.