I am a research student and am really new to the world of bioinformatics. I am working with 40 ovine fecal samples which are suspected of scouring. In this I have about 6 variables (collection time, evidence of scouring, stool consistency, sex etc). I have successfully followed the “Moving Pictures” tutorial - and have demultiplexed, ’ deblurred’ and then run the various commands. I need help now with interpreting the outputs.
Specifically, for two parts. I am not sure how to visualise the “Most Abundant Features/AVS” - I have used qiime taxa collapse down to level 2, and have 24 features in the collapsed-table-summary.qzv. I am unsure of now how to visualise this into a graph/bar plot? Would interpreting this into a simple bar plot be suffice?
My goal is to get some form of visualisation of the most abudant features, so I can interpret this further in my thesis. I know previously in qiime1 there was an output for “Most Abundant OTU’s” - and have seen Spearman’s Correlation analysis been used to interpret. I know this is not possible with Qiime2. This brings into my next question:
ANCOM, I have done a quick crash-course on ANCOM and have managed to run a few commands to ANCOM analysis on the variables I listed above, which I have also collapsed into Level 4 qzv. files. I am having a really hard time understanding how this contributes to my analysis (I understand it is indicative of composition of samples) but I am not sure how this can help further with relative abundance of taxa, as I can only get output per variable, not on all 40 samples.
Sorry if this doesn’t make sense, I am still learning the jargon!