Hi everyone,
I’m trying to use MetaPhlan for microbial profiling on RNA-seq data, and I have some issues while tweaking the parameters. Do you have any suggestions for a run in this context?
Also, specifically for my samples, I expect to have a low abundance of non-human transcripts. Are there specific suggestions for this case?
I tried a run with default parameters and no results were retrieved. I saw in many other posts that people tweak the --stat_q parameter, which I had to lower to 0.01 in order to see some results. But I’m now worrying of having found false positives.
Are there other thresholds I could set? Like the --perc_nonzero parameter, which it’s not clear to me, or others?
Ideally, I would want a threshold on the minimum number (or percentage) of clade-specific marker genes that need to be covered by my samples’ reads in order for that clade to be returned. Is there something like it?
Many thanks.
My MetapPhlAn: MetaPhlAn version 4.0.6 (1 Mar 2023)