filter_samples_when???

[jwdebelius (Justine Debelius)]

Hi @Aakash_Mantri,

I would do this after deblur. ...I might actually calculate your distance matrices before doing it. It will not change the results of deblurring.

You may. also find some of these threads useful:

Filtering samples and seqs for downstream analysis

Question: I have imported, demultiplexed, and denoised a set of 16S V4 amplicon sequences using 515F–806R primer. I realized at this point that half of my samples are DNA and half of them are cDNA (from RNA) and I just want to focus on the DNA samples. Reading the forums and the filtering tutorial, I figured out that I could run qiime feature-table filter-samples with a metadata file containing just the sample ids that I want to keep. So I subsetted my metadata file (‘mapping_file_16S.tsv’) to …

Alignment/Tree Building and Filtering samples

Hello Emily, This is a tricky question. The basic answer is that the exact tree you build will depend on the microbes included in the MSA, so it probably best to split up your samples, remove any OTUs that don’t appear in a cohort, then built one tree for each cohort. However, the same is true of OTU clustering; the mixing cohorts will effect the exact OTUs that appear in each one, so your cohorts a little bit mixed-up no matter how you build the tree. Short answer: either way would work OK… …

Mistake in metadata file and re-running core metrics analysis.

Hi @xchromosome, I’m just going to preface this with “maybe you want to get a cup of coffee ” because it seems like a long answer as I write it. Im also going to apologise for my spelling mistakes in advance, because I know I will not see all of them until the post gets locked in like a month. So, first, if I’ve made a typo related to treatment or timepoint, I apologize. This depends on your hypothesis, so I’ll leave that judgement to you. I also think it might help if you understood…