MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks
Apache License 2.0
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docs/readme/peaks.md disconnect example / arguments #88

Closed emiraldi closed 2 years ago

emiraldi commented 2 years ago

@tacazares The "maxatac peaks" example given in peaks.md is missing several of the purportedly required arguments. For example, cutoff_value, cutoff-type and cutoff_file are not specified (I think these are actually optional, given assumed maxatac_data structure and max f1-score default). In addition the command includes an undocumented argument "threshold". Please review!

emiraldi commented 2 years ago

For "maxatac peaks", I bet more people will use this function for prediction versus benchmarking. For that reason, I wonder if it might be better to make the --bin_size default maxATAC resolution 32bp.