Enhancements: sex chromosome predictions

MiraldiLab / maxATAC

Transcription Factor Binding Prediction from ATAC-seq and scATAC-seq with Deep Neural Networks

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Enhancements: sex chromosome predictions #83

Closed emiraldi closed 2 years ago

emiraldi commented 2 years ago

Let's evaluate performance on X and Y chromosomes, as there are some important genes (especially for the immune system) on chromosome X! Would be good to provide this capability.

tacazares commented 2 years ago

I think the main limitation of this would be that we do not consider the X or Y chroms during normalization so we have excluded those data from our current files.

emiraldi commented 2 years ago

@tacazares Will 'maxatac predict' work if the user specifies x or y chromsomes? If not, we should highlight this in the 'maxatac predict' documentation, to avoid error messages. If 'maxatac predict' does work with x and y chromsomes, then we should include a "warning" that we have not benchmarked on chr x or y but will soon.