I referred to the documentation (filter-samples: Filter samples from table — QIIME 2 2024.10.1 documentation) and reviewed the table.qzv file from the Moving Pictures tutorial, but I couldn’t understand how they determined the value of 1500. Could you please help me understand how to decide on the appropriate parameter value?
Hello!
By executing this command, you are filtering out all the samples that have total frequency less than 1500 reads.
One just needs to decide which samples should be kept for the analyses. For example, I prefer to have at least 3000-4000 reads per sample. However, if all my samples have more than 8000-10000 reads, and only one 3000, I would set minimum frequency to any value between 3100 and 7900 to filter out sample with 3000 reads and keep only samples with higher frequencies.