About

• In this project i attempt to reproduce the pseudogene_model from 'Evolutionary informed deep learning methods for predicting relative transcript abundance from DNA sequence' by Jacob Washburn et al.
• Some slight modifications are made where necessary. Python version of some scripts are provided. Those scripts in which python lacks suitable implementation, i retain the R versions.

Making BSgenome.ZM.v3.31

• Download Zmays_v3_seed

• from R studio console type

1. library(BSgenome)

2. forgeBSgenomeDataPkg('path/to/seed_file', 'path/to_save/source_tree')

• from terminal

3. $cd 'path/to_save/source_tree'
4. $R CMD build BSgenome.ZM.v3.31
5. $R CMD install BSgenome.ZM.v3.31_1.0.tar.gz

• Now running Get_pro_and_ter.R

• cheers