Do I need to go back and filter my long-reads?

Question

[eesiribloom]

A while back I asked about filtering basecalls from dorado. I was taken up with other projects so am only returning to this particular dataset now.

I took people's advice and did not filter my data and aligned to human reference genome GRCh38. My most recent samples have higher basecall quality and better alignment but the older samples have more of a tail (see violin plot below).

Is this good enough or should I filter my data e.g. for basecall quality > Q9 ?

[GenoMax]

Is this good enough

You need to make the call. We don't know what you are planning to do with this data downstream.

older samples have more of a tail

That is a characteristic of the sample (assuming same experimental procedure and flowcell/pore, dorado model was used). You could track it as a batch in case that has any effect on the analysis later.