Coverage Thresholds

[Ana]

I am running panphlan_profiling, but am getting no results on my samples. I need some help determining thresholds. I tried the defaults suggested --min_coverage 1 --left_max 1.70 --right_min 0.30, and other variations. Please help.

STEP 3: Strain presence/absence filter based on coverage plateau curve…
[I] Minimum median coverage threshold: 1.0
[I] Left maximum plateau threshold: 0.3
[I] Right minimum plateau threshold: 0.3
[I] Maximum zero non-plateau threshold (multistrain detection): 0.2
[I] Bacteroides_fragilis.tsv median coverage: 93.68; left-side cov: 2.38; right-side cov: 0.62; out-plateau cov: 0.36
Bacteroides_fragilis.tsv: no strain detected, sample does not pass LEFT-side coverage threshold.

[leonard.dubois]

Hi, to better understand the PanPhlAn thresholds, maybe this post could help you

PanPhlAn threshold selection

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:

Missing sample from the panphlan profile step

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
Léonard