Iām so sorry, probably Iām confused and I donāt know how answer to these questions because I donāt well understand that means filtered by prevalence.
I understood that is referred to samples but I donāt understand very well the meaning.
Within the docs for this command, this is how the prevalence parameter is explained: "The minimum portion of samples that a feature must have a relative abundance of at least abundance to be retained." Does this definition make sense to you?
After reading the linked resources, Lets try answering the questions:
What would filtering by prevalence do?
Why do you want to filter by prevalence?
What does setting a prevalence of .34 do?
Thank you so much for your precious help like always!
After reading, maybe prevalence is the percentage of samples that have 1% of abundance? If I selected 1% of abundance of course.
So, if I put 1% of abundance and 34% of prevalence this means that I remove the ASVs that are less than 1% of abundance and are present in 34% of samples?
So, if I reduce the percentage of prevalence (probably 5-10%) can I maintain more samples?
Did I well understand ?
If I put 1% of abundance and 10% of prevalence I remove the ASVs less than 1% only in 10% of samples?
You will retain more features. You will lose samples if a sample has no features that meet the criteria, which might have been happening with your first parameters!
You are 100% right! Just to rephrase
It will be removed if the ASVs is less then 1% abundance or in less then 10% of samples. Similarly, For a ASV to be retained it has to be equal to/greater than 1% abundance and equal to or more then 10 % of samples.
I agree has a percentage below 1%
d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Myroides | 0.976%
and your provenance says that you did filter on 1% abundance
Could you send me the table you got as an output for: qiime feature-table filter-features-conditionally?
Hi @Linda_Abenaim,
I misunderstood how filter conditionally works!
At one point I said:
I was wrong
The prevelance/abundance filter just says its at least 1% in at least 10% of samples. Meaning that if its 1.0% in 10% of samples and 0% in the other 90, that gives a relative abundance of like 0.1% overall. So I believe that you used the command correctly, our understanding of how it filtered was just off!
So if I want to remove the ASV that are less than 1% of abundance what do you suggest to do?
I want to do this only for the visualization on taxa barplot.
Or maybe it is important also for ANCOM bc..
But for that moment I just want to remove the ASV that are less than 1%.
@Linda_Abenaim,
I am not sure that qiime has that either.
It is a little bit difficult to do grouping like this because if feature 1 in sample 1 had a 20% relative abundance, but feature 1 also had a relative abundance of 1% in sample 2. Would you want feature 1 to be collapsed into other because it has a low abundance in sample 2? I don't think so because you would be missing feature 1's large presence in sample 1. This is what I mean about you wanted to filter on relative abundance per sample.
I would suggest reading the methods of the papers you saw that visualization in and seeing if you can follow their methods! Just make sure to cite them if you do!