Good morning QIIME2 team!
My previous work has focused on metagenomic and 16S sequencing of the rumen microbiome. However, we have begun to work with some more challenging samples in terms of abundance, etc. Recently, we had a set of sheep milk samples sequenced and I wanted to get a few opinions from this group.
This is 16S data that was put on a Nano-run just to evaluate how the sequences looked as we had high cluster density but only 55% of the clusters passed filter. I didn’t expect things to go smoothly with milk samples and expected large variation but attached is the table-paired-end qzv and as you can see we have HUGE variation. Samples #52 and #69 are our controls (water and zymogen community) but all others are milk samples. Any advice as to where you would set sampling depth for this type of data? Would running on a full lane improve this output?
Thank you for any and all advice on this matter!
table-paired-end2.qzv (559.7 KB)