snapATAC multiple sample integration

[afcmalone]

Hi, When I try to apply snapATAC to my data I get errors. What I am trying to do is integrate 3 datasets (all from same 10X method – 3 separate samples – I have made 3 different snap files). I have then followed your ‘Integrated analysis of 10X and snATAC’ pipeline - https://github.com/r3fang/SnapATAC/tree/master/examples/10X_snATAC successfully (I think) – However when I try to use this integrated snap object (x.after.sp) for further analysis such as ‘gene based annotation’ - step 9 of ‘https://github.com/r3fang/SnapATAC/tree/master/examples/10X_brain_5k’ I get an error –

x.sp = addBmatToSnap(x.sp); Error in addBmatToSnap.default(x.sp) : bins does not match between snap files, please regenerate the cell-by-bin matrix by snaptools

Any ideas where I have gone wrong. Perhaps I have not created the integrated snap object correctly? (however followed your pipeline as explained above)

Any help would be much appreciated!