Scenic Byways Massachusetts. So, for each sample, I have bins that are not dereplicated and not f

So, for each sample, I have bins that are not dereplicated and not filtered. OTU_table ( otu id and the sample identify). OTU_mapping file (OTU_id, acc, full_name, taxonomy) Sample mapping file (ids, type, etc) According to the tutorial, I first generate a biom file with Oct 19, 2025 · Hello, I am performing a study about differences in microbial communities between two sample types in an Antarctic ecosystem. Namely, when I try to install it using "devtools::install_github ("jbisanz/qiime2R" I get the following error: Oct 19, 2025 · Hello, I am performing a study about differences in microbial communities between two sample types in an Antarctic ecosystem. 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). 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. Aug 11, 2025 · This topic was automatically closed 31 days after the last reply. The sequences are forward and reverse and look like this: @SRR8243471. Jan 8, 2022 · 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): Mar 23, 2023 · UTSA is a public research university and a Hispanic-Serving Institution located in scenic San Antonio, Texas. I have created my phyloseq object using the following R code: physeq_21<- qza_to… Aug 11, 2025 · This topic was automatically closed 31 days after the last reply. My plan is to import all the bins together into Qiime2, filter Apr 21, 2025 · Hi everyone, I have just finished going through my qiime2 analysis following the moving pictures and fecal sample tutorial (for merging). I fallowed this installation guide GitHub - lozuponelab/q2-SCNIC: A QIIME2 plugin for running SCNIC and it has been installed successfully. My plan is to import all the bins together into Qiime2, filter Aug 17, 2021 · I'm new to using QIIME2. 1 1 length=301 . New replies are no longer allowed. Apr 21, 2025 · Hi everyone, I have just finished going through my qiime2 analysis following the moving pictures and fecal sample tutorial (for merging). Now, I receive some datasets from collaborators. Namely, when I try to install it using "devtools::install_github ("jbisanz/qiime2R" I get the following error: Oct 24, 2017 · Hi, I am beginning to use Qiime2, and I try to do the diversity analysis. Mar 31, 2025 · Dear devs, dear users I am processing metagenome dataset. However, when performing differential abundance analysis (Tried ANCOM and LEFSE so far) and performing Holm p-value correction, I detect zero significantly different Dec 3, 2025 · Hi, I want to profile the protist community in the rhizosphere, can I use silva database as listed following? Jan 8, 2022 · 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): Mar 23, 2023 · 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. However, when performing differential abundance analysis (Tried ANCOM and LEFSE so far) and performing Holm p-value correction, I detect zero significantly different Oct 16, 2025 · Basubi: I merged library A + B → richness stays ~350 (fungi) / ~300 (bacteria). Feb 13, 2020 · I have a problem with the installation of package. According to PERMANOVA, there are significant differences between communities of the two sample types. The aim is to discover the relationship between the diversity and the status. I have installation problem with q2-SCNIC now. I have created my phyloseq object using the following R code: physeq_21<- qza_to… Aug 17, 2021 · I'm new to using QIIME2. 1 1 length=301 Jan 8, 2022 · 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): Mar 23, 2023 · UTSA is a public research university and a Hispanic-Serving Institution located in scenic San Antonio, Texas. Mar 21, 2022 · Hello everyone, I have downloaded some sequences from NCBI and I am having some troubles uploading them into qiime.

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