I have a quick question regarding the bioinformatics of various libraries. In my case, I just received the data for 2 libraries and have performed the denoising step. I saw on this tutorial , that I have to merge the the outputs from the denoised data set first and then proceed with the analysis.
I have merged both libraries FeatureTable[Frequencies] and FeatureData[Sequences] and then ran code bellow to get the taxonomy output. Everything seems to be working well, but when I looked at the jaccard_emperor.qzv (897.4 KB) , I can see that the data clusters, but it is clustering along 4 sections, (burned, unburned, burned, unburned).
*I displayed the plot showing: Color = sites (Site 1-6 red(burned), Site 7-9 (green) unburned) and when I go under the visibility tab, and I un-click burned/unburned the corresponding colors disappear).*
I am assuming I did something wrong, since it seems like it is because of the 2 different libraries, but I am not sure if this is the case, and or not. Could you please let me know if what I did makes sense. I can also send you other code and or files if you need to see them.
Thanks in advance
Code for merging data
*qiime feature-table merge *
*qiime feature-table merge-seqs *
Code for taxonomy
qiime feature-classifier classify-sklearn
–i-reads DADA2/Fungal-RepSeqsMerged.qza \ #merged rep-seqs
–p-read-orientation reverse-complement \ # I am working with the ITS2 primers
–o-classification Fungal-taxonomy-paired-RC.qza \ #output