Anthony Tan

Which link are you referring to?

**Self** promoter elements having a score of 1 was an intentional change in the latest versions of ABC. To reproduce the 2021 paper, you'd have to go to a previous...

The threshold varies based on your inputs. See https://abc-enhancer-gene-prediction.readthedocs.io/en/latest/usage/methods.html#interpreting-the-abc-score

> EnhancerPredictionsFull_threshold0.02_self_promoter.tsv is generated by selecting subset of enhancer-genes pairs with ABC.score > 0.02 from EnhancerPredictionsAllPutative.tsv This should be true: https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/main/workflow/scripts/filter_predictions.py#L50. Can you show your results with ABC scores <...

Yes, the filtered file also removes self promoters. Take a look at that [script](https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction/blob/main/workflow/scripts/filter_predictions.py) as it outlines exactly how it goes from the all putative file to the thresholded file.