Genrich for ATAC-seq Analysis with Covariates

[dxkeac]

I have been using your excellent software, Genrich, for ATAC-seq analysis, and I truly appreciate its robustness and utility.

I have a dataset consisting of 7 control samples (including both male and female) and 5 patient samples with psychiatric conditions (also including both male and female). I am wondering if Genrich is suitable for analyzing such a dataset where sex or other factors might act as a covariate in addition to the primary condition of interest.

Would you recommend any specific considerations, preprocessing steps, or alternative approaches for handling this type of dataset using Genrich?

Thank you in advance for your guidance!

[jsh58]

Your use of the word "control" is different from how Genrich is programmed to analyze controls, so please review the README and previous issues (#19, #74) for clarification.

In cases with mixed genders, you should consider using the -e argument to eliminate the sex chromosomes from the analysis.