Hi guys. I have just recently learned how to use a QIIME2’s pipeline to do a part of my research study. The pipeline I used was found in the “Moving Pictures” tutorial. In my study, I have 14 samples which were analysed using that pipeline. 4 of the sample ID starting with E7, F7, G7, H7 were negative controls, so they were supposed to have no bacteria found in them. But when I got the taxa-bar-plots.qzv from Taxonomic analsysis, 3 of the control samples showed contamination with some bacteria. From the same graph, I found that the type of bacteria that had been contaminated with in each sample was:
E7-S505-N706 | k__Bacteria;p__Actinobacteria;c__Acidimicrobiia;o__Acidimicrobiales;f__SC3-41;g__;s__ | 100.000%
F7-S506-N706 | k__Bacteria;p__Cyanobacteria;c__Chloroplast;o__Stramenopiles;f__;g__;s__ | 100.000%
G7-S507-N706 | k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium;__ | 100.000%
My question is that, if there is a command or a pipeline where I can remove those three bacteria in all of the 14 samples, or if such a process is possible. I have tried to look around on the site but I couldn’t really find any. My reason is that the 3 contaminating species would likely also be found in the other samples where they shouldn’t be found if the samples were not contaminated. So I need to remove the 3 species in all my samples, then run through the pipeline again now with samples in the de-contaminated state. The end result I would like is in the new taxa-bar-plots.qzv graph, I should have an empty value in all the 4 controls.
Thank you for your contribution!
I have also included FeatureID (that I found in the "Moving Pictures" tutorial of the 3 contaminating bacteria, though am not sure about its relevance for this process.