Hi everyone,
Has anyone here tried performing functional analysis using outputs from the EMU pipeline (for 16S taxonomy assignment)? I’m particularly interested in linking EMU's species-level taxonomy to predicted functions (e.g., metabolic pathways).
What tools or pipeline did you use for this? Any tips or workflow suggestions would be really appreciated.
Thanks in advance!
•
written
by
henrique.mouradias •
1 answer
You can't use EMU with tools like PICRUSt2 because it doesn't produce typical outputs such as OTUs or ASVs. EMU works more like a read-level classifier to compute species abundances.
For long-read 16S rRNA metabarcoding, you need a pipeline that provides representative sequences for each species, eg LACA (https://www.biorxiv.org/content/10.1101/2023.11.26.568539v1)
Log in to answer this question.
-
Reproducing a published rice salt-stress RNA-seq analysis from FASTQ: feedback on workflow choices?
written by chirag •
-
Hello, I analyzed ONT 16S amplicon data using the EPI2ME workflow with Minimap2, but the output doe…
written by Ramen •
-
Assembling a chloroplast genome using only PacBio data (Illumina reads lost)
written by Serena •
-
Kraken2/bracken with 16S sequencing downstream analysis
written by Isidro •
-
Multiple taxonomy hits per OTU ID in VSEARCH despite --top_hits_only (90% ID after QIIME2 clusterin…
written by salma.sarker •
-
How to Perform Lineage Analysis Using SNPs Derived from a De Novo Assembly?
written by alex •
-
Best Practices for Tumor-Only WES Data Analysis: Seeking Feedback on Variant Calling Pipeline
written by George •
-
How to Obtain a GMT File for Pathway Enrichment Analysis in Gallus gallus Metabolomics Data?
written by DareDevil
-
Bacterial metatransciptome antimicrobial resistance genes workflow?
written by SushiRoll •
-
How To Perform A Pathway Or Network Level Analysis Of Rare Variants?
written by ewre
