Prediction using sequences (vep_cli_seq.py)

[pyareedash]

Hi developer,
A few queries while using vep_cli_seq.py in Sei-Framework,

What's the difference between chromatin_profile_ref (line 28) and chromatin_profile_ref_adjust (line 31)?

Is there a way to extract column names for chromatin_profile_file and sequence_class_file?

Thank you :)

[kathyxchen]

Hi,
chromatin_profile_ref is the chromatin profile predictions made by the Sei deep learning model and chromatin_profile_ref_adjust is an adjustment on specific histone mark related profiles to normalize for the effects of nucleosome occupancy. You can read more about why we do this adjustment in the manuscript methods section.

The column names are in the model folder target.names and seqclass.names

[pyareedash]

Hi,
Thank you!