Error estimating distance parameter value in Cicero

[Stella Kyomen]

Hi, 

I want to use Cicero to get co-accessibility scores of scATAC-seq data from mouse tissue. I keep getting the following error:

Error in estimate_distance_parameter(cds, window = window, maxit = 100, :
No distance_parameters calculated

I tried to change window and distance constraint but still got the same error, even when decreased sample_num to very low values. Does anyone have a clue of what else I could change?

Thanks

Cheers,

Stella

[hpl...@gmail.com]

Hi Stella,

Sorry for the delay. Can you try setting the max_sample_windows to something larger (1000)? Also, is your data particularly dense? If so, you may need to raise the max_elements parameter. 

Hannah