olechnwin

Sorry for the different scenarios back and forth with CHM1 demo and my own data. I hope it's not too confusing. But, I was able to get the SequenceTube displayed...

> I think you need to manually check how many groups are there in your data. > > ```r > col.partition=c("group1" = "red", "group2" = "blue") > ``` > >...

Ok. I may have found why the discrepancies. The reason why I cannot find the rep2 peak with exactly the same location was because there are several rep2 peaks that...

I just posted discrepancies that I found in the output. Your issue is also concerning. I would thought they should be give the same IDR regardless of the order. Have...

Hoping for insights for this issue too...

How do you use the kde2d method? I've downloaded the latest version of this package from github but `geom_pointdensity` still do not have method parameter?

@fenderglass, I don't know how the pull works. But, I just posted the same request [here](https://github.com/lh3/minimap2/issues/834#issuecomment-1131677329). It would be great if sequences for secondary mapping can be turned on. Thanks!

@annsophiegironne, ecoli is my spike-in. I aligned my reads to each genome individually. ecoli_filterdup.bed was the output from running macs2 filterdup.

@ktrns and @JoseEspinosa, This may be a silly question but in the region that is shown above, we are assuming the depleted region between the two peaks is where the...