Snakemake pipeline for Transposable Elements quantification and Differential Expression analysis

• DropSeq
• Bamtools
• STAR
• bedtools
• R
• samtools
• fastqc

Before running, you need to set the config.yaml , where you need to set the paths to the STAR genome index and othe files that are required. Also you can set there the contrast (for differential expression analysis) and the number of cpus to be used by single tools.

You can build the container available here. Follow the istructions found in create_cont.sh. One you have your sif file you run the pipeline by moving to the directory whre you downloaded it and run:

    snakemake -j10 --use-singularity

Where 10 is the max number of cpus that snakemake will use. And the outputs will be stored in a directory named results.

Davide Bressan - Fulvio Chiacchiera Lab

Some parts of the code where taken from the amazing work of Daniel Fernandez Perez. Specifically, from his repository: Rna-seq pipeline