Hi, maybe this post could help you:
Hello,
sorry for the late answer, I was away from work the past week.
First, thanks a lot for these detailed and relevant questions. I’ve actually never seen such way of visualizing PanPhlAn intermediate results, it is very interesting.
So let’s talk about the thresholds and their role first
Actually PanPhlAn provides a way a visualizing mapping results as coverage curves. This is an example coming from PanPhlan tutorial (not normalized)
[image]
I find this kind of visualization more usefu…
Or this channel:
Dear authors,
I find both PanPhlAn and PanPhlAn3 might missed some samples in the panphlan profile step.
In PanPhlAn, sometimes it will report errors like:
[TERMINATING…] /usr/local/bin/panphlan_profile.py, 0.23 minutes.
QUALITY WARNING: sample GCF_000598405_errfree_r0 may contain multiple strains, PanPhlAn extracts the dominant strain
QUALITY WARNING: gene-families of sample GCF_000598405_errfree_r0 may come from multiple strains
number of gene-families: 6739 is 10% higher than expected n…
Let me know if they are not answering you problem
Have a nice day