Choice of Peak files to use in chromVAR analysis

[sylestiel]

Hi,

Would you recommend using the peaks.bed file in the general outs folder or that in the filtered_peak_bc_matrix sub-folder for chromVAR?

Are their advantages to using aggregated peak file vs the alternative?

Thanks!

[jgranja24]

Hi @sylestiel,

The Greenleaf Lab recommends using ArchR https://github.com/GreenleafLab/ArchR to identify peaks and many of the chromVAR features are available there.

We recommend fixed-width peaks which are not generated from 10x output.

Hope that helps!

[sylestiel]

Can we still start the analysis by using Cell Ranger output files?