RAN-Seq-Snakemake

RNA-Seq analysis for cod (gadus morhua) workflow with help of Snakemake

Snakemake environment setup

Install miniconda and set up Snakemake environment according to Snakemake Tutorial.

Note: The environment for our RNA-Seq Snakemake can be found in the root repository.

Reference

This workflow was applied in:

Yadetie, F., Zhang, X., Hanna, E. M., Aranguren-Abadía, L., Eide, M., Blaser, N., ... & Karlsen, O. A. (2018). RNA-Seq analysis of transcriptome responses in Atlantic cod (Gadus morhua) precision-cut liver slices exposed to benzo [a] pyrene and 17α-ethynylestradiol. Aquatic Toxicology, 201, 174-186. https://doi.org/10.1016/j.aquatox.2018.06.003