- 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.
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Download Zmays_v3_seed
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from R studio console type
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library(BSgenome)
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forgeBSgenomeDataPkg('path/to/seed_file', 'path/to_save/source_tree')
- from terminal
- $cd 'path/to_save/source_tree'
- $R CMD build BSgenome.ZM.v3.31
- $R CMD install BSgenome.ZM.v3.31_1.0.tar.gz
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Now running Get_pro_and_ter.R
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cheers