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cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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[Cicero in GM12878/K562 cell lines data ] #81

Closed dhoneyi closed 2 years ago

dhoneyi commented 2 years ago

I would use Cicero to calculate co-accessibility score in GM12878 scATAC-seq dataset. Since the GM12878 is cell line data, I wonder why can I used Cicero on cell line dataset. For example, I have a GM12878 data containing ~20,000 cells and ~240,000 peaks. Or can you share me the co-accessibility scores information in your Pliner et al., 2018, Molecular Cell 71, 858–871. Thanks!

hpliner commented 2 years ago

Hi, you can use Cicero on cell line data in the same way you would with any other data. See the instructions here: https://cole-trapnell-lab.github.io/cicero-release/docs_m3/

The scores from GM from the original paper are available as a gzipped csv here: https://drive.google.com/file/d/14Mfs6vlKX8tQGRnEpl_xPpPHo33nIgAB/view?usp=sharing