how to find out the ccan including one peak of my interest

[Pengxin Yang]

Hi  Hannah,

Thanks for developing this great tool!

I am wondering how could be find out the matching ccan for a specific peak of my interest. 

For example, I identified 95 ccans on chromosome1. "chr1-222222--33333" is a peak that I would dig into. How could I find out the ccan that this peak belongs to?

By the way, which parameter should i use if I would like to include both upstream and downstream 1000000bp of TSS of a gene when it comes to the ccan generation?

Thanks

Best

Penny

[hpl...@gmail.com]

Hi Penny,

The CCAN assignments are in the output of the generate_ccans function, so you can just look at that output dataframe to find out which ccan that peak is assigned to. If the peak is not in the dataframe, it means that that peak was not assigned to a ccan.

To include more upstream and downstream sites, you need to rerun cicero to with higher values for the window and distance_constraint and then rerun generate_ccans. See details here: https://cole-trapnell-lab.github.io/cicero-release/docs/#running-cicero

Best,

Hannah