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q2-SCNIC installation - Library Support - QIIME 2 Forum I'm new to using QIIME2 I have installation problem with q2-SCNIC now I fallowed this installation guide GitHub - lozuponelab q2-SCNIC: A QIIME2 plugin for running SCNIC and it has been installed successfully
how to reference the plugins used - QIIME 2 Forum I wanted to ask if anyone can help me to know how to cite the qiime plugins (permanova, shannon, observed features, evenness, faith phylogenetic tree, braycurtis, scenic plugin, taxa barplot, and picrust2) See this page for more details and an example (that covers some of the methods you mentioned):
PhD Opportunity - Soil Microbial Ecology - QIIME 2 Forum UTSA is a public research university and a Hispanic-Serving Institution located in scenic San Antonio, Texas The main campus, where the graduate position will be housed, enrolls ~34,000 students and has a diverse set of collaborative groups spanning ecology, microbiology, geosciences, and natural resource management
UBC Okanagan, Quantitative Ecology - QIIME 2 Forum Situated in the heart of the Okanagan Valley, one of the most scenic regions in Canada, it offers an intimate learning environment and excellent opportunities for regional, national, and international scholarly activities Biology, at UBC's Okanagan campus, is housed in the vibrant Irving K Barber School of Arts and Sciences
Importing bins mags into Qiime2 - Technical Support - QIIME 2 Forum Dear devs, dear users I am processing metagenome dataset I currently follow the q2-moshpit: A set of tutorials showcasing shotgun metagenomics analysis workflows, but I modified some steps I assembled metagenomes and binned samples outside of Qiime2 So, for each sample, I have bins that are not dereplicated and not filtered My plan is to import all the bins together into Qiime2, filter
Unnasigned ASVs at lower taxonomic ranks can alter metrics of alpha and . . . I understand and agree with the idea that unclassified ASVs are also informative and their elimination wastes valuable information However, these sequences without a clear taxonomic assignment (i e from family to lower taxonomic ranks ) would not disrupt the phylogeny of a particular group of samples and therefore the alpha and beta diversity metrics that incorporate phylogenetic distance as
Observed ASV richness drops after adding 3rd MiSeq library — why do I . . . Basubi: I merged library A + B → richness stays ~350 (fungi) ~300 (bacteria) But when I merge library C with A+B the observed ASV richness drops for both kingdoms (I lose ≈100 ASVs for bacteria and ≈100 ASVs for fungi — final counts ~200 bacteria, ~250 fungi)
PERMANOVA results significant, but differential abundance results . . . Hello, I am performing a study about differences in microbial communities between two sample types in an Antarctic ecosystem According to PERMANOVA, there are significant differences between communities of the two sample types However, when performing differential abundance analysis (Tried ANCOM and LEFSE so far) and performing Holm p-value correction, I detect zero significantly different