Need for peak re-calling after Cell Ranger arc v2?

[AmelZulji]

Hi there, I was wondering whether peak re-calling using MACS2 as described here is still beneficial given that CellRanger arc v2 has improved the algorithm as described here?

Thank you for help!

[ShanshanHe-44]

That is an interesting discussion. I am also curious about the performance of the updated CellRanger v2 compared with MACS2. The current peak calling vignette here is still using the PBMCs 10k dataset based on CellRanger pipeline version 1.1.0. From the coverage plot, the MACS2 peaks appear to be more precise. However, I am also interested in how CellRanger v2 performs.
As far as I know, CellRanger v2 doesn't include the summit position of each peak, whereas MACS2 does. So, if your research interest is understanding motifs, MACS2 might still be the better choice.