Should I do rarefaction before compute alpha and beta diversity in 16S anlaysis?
Hi all, when doing 16S analysis in QIIME2, should I do rarefaction before calculating the alpha and beta diversity. There are a lot of debates on this question.
microbiome
16s
rarefaction
• 954 views
•
link
written
by
932477002 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
How to export high-resolution figures from QIIME2 visualizations for publication?
written by Pluton17 •I am preparing a manuscript on the metagenomic analysis using QIIME2, and I'm facing issues with figure quality. My problem: I have QIIME2 visualization files …
-
Kraken2/bracken with 16S sequencing downstream analysis
written by Isidro •Hello everyone, I’m working on a 16S rRNA microbiome project using Kraken2 with the SILVA database for taxonomic classification. After classification, I apply Bracken to …
-
Tool: MicrobiomePhylo: A Comprehensive Platform for Advanced Microbiome Amplicon Sequencing Data An…
written by camillatafuro •Hi everyone! We've launched [MicrobiomePhylo][1], a cutting-edge web application designed to empower researchers in the field of microbiome analysis. Our platform offers a comprehensive suite …
-
Should I calculate beta diversity with or without rarefaction?
written by dpcHi there!!! I am doing metagenomic analysis with metaphlan output data that show relative abundance s of the species. I am going to calculate the …
-
Softwares for statistitical analysis of MetaPhlAn output
written by dpcHi community!!! I have profiled shotgun metagenome data with MetaPhlAn. Now, I want to do statistical analysis (e.g. alpha-, beta- diversity comparison, rarefaction graph, boxplots, …
-
How to rarefying 18s rDNA data?
written by 1713307477 •I have one raw otu (**without rarefying**) about 18s rDNA from ocean samples. I only want to analyze the alpha and beta diversiyt of **phytoplankton** …
-
Qiime2 - make table.gza
written by agata88Hi all! I am new with Qiime2 and any kind of help would be much appreciated. I have abundance results for every taxonomy (phylum - …
-
metagenomics- read based diversity analysis
written by biobiuI'm interested in alpha and beta diversity analysis based on read based and marker gene methods. Is there any recommendations on tools or pipeline that: …
-
Diversity analysis after metaphlan2
written by biobiuHi, I've ran metaphlan2 on shotgun metagenomics sequencing data and want to perform diversity (alpha and beta) analysis. Is there some tools allows calculating alpha …
-
alpha-diversity beta-diversity rarefaction curves
written by agata88Hi all, I am new in this kind of analysis. Maybe somebody could explain me (like for a child) what is exactly alpha-diversity, beta-diversity and …