ISM using REF and ALT sequences as baseline

Feedback & Feature Requests
1

Hi!

I’d like to perform ISM using both REF and ALT sequences as the “baseline”. The idea would be to identify the disruption / appearance of new TF motifs or patterns, just like you did in Supplementary Figures 6-8 in the manuscript and mentioned in the methods (Comparative ISM for Variant Effect Interpretation).

Is there an alphagenome-friendly way to set the ALT sequence as a reference for the ISM analyses or do we need to implement it ourselves for now?

(Thanks a lot guys, the tutorials are amazing!)

2 Likes
2

Hi @Marc_Pielies_Avelli,

Currently we don’t have a way to provide a custom sequence to do ISM, beyond providing ALT/REF mutations via the Variant argument. We will try and do this ASAP though!

Thanks

Tom