Hi everyone, I was asking to Daniel in the github issues some questions on how to approach when you have AA reference sequences and want to explore metatranscriptomic (NT) reads: https://github.com/nf-core/phyloplace/issues/18#issuecomment-2657251266 From what you were saying @Daniel Lundin, you would use the

FeatureCounts

output from

metatdenovo

as a quantification then, after obtaining the ORFs and placing them. That makes quite a lot of sense. Since I was coming from the approaches made by

gappa

and

EPA

that focus mostly on placing reads I did not think on this approach. The ORFs however could be included directly in the alignment and tree avoiding EPA no? Or this would make everything slower. Thanks for your time!