Models of all ENCODE cell lines generated using TREDNet are stored in CenTRED directory (separately for hg19 and hg38 build) .
/data/Dcode/common/CenTRED
/net/intdev/devdcode/common/CenTRED
Master control file was generated using a perl script /net/intdev/devdcode/common/CenTRED/training_files/generatebk_di.pl
Positive and control files were generated using generate_training_files.sh
Models for both builds and corresponding training files are located in respective directories in /data/Dcode/common/CenTRED/
Scripts for model training and batch submission are also available in aforementioned directories.
As of now, for hg38 we are using draft phase 1 model that Sanjar trained. It is located in /data/Dcode/common/CenTRED/TREDNet/v0.1
Finally, the ENCODE metadata for these models is described in this file: https://docs.google.com/spreadsheets/d/1SvqMhg5HN1UzXoaJaFQwS2k-Zir3HZBy/edit?usp=drive_link