Comparing ATAC-seq narrowPeak Files from Chicken and Mouse

Question

[Rafael Soler]

Hi everyone,

I'm working on a comparative analysis of ATAC-seq data from Chicken and Mouse samples. Specifically, I have narrowPeak files for both species and I've successfully used the liftOver tool (with minMatch=0.5?) to map the Chicken peaks to the Mouse genome.

To perform a statistical comparison following the csaw analysis pipeline, I understand that I need the original BAM files. However, these BAM files are not suitable for liftOver since they contain read mappings rather than peak coordinates.

I'm at a crossroads and would appreciate some advice on how to proceed. Here are the options I'm considering:

1. Using another statistical tool: Should I explore a different tool that can work directly with the liftover narrowPeak files without needing BAM files?
2. Transforming the BAM files: Is there a way to convert or remap the BAM files from Chicken to Mouse that would allow me to use them in csaw?
3. Alternative approaches: Any other recommendations or workflows that could facilitate a comparative analysis of the liftover narrowPeak files?

Any guidance or suggestions on the best approach for this analysis would be greatly appreciated.

Thanks in advance for your help!

Best regards,
Rafa