dada2
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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
Good day, I hope you are all well. I'm opening this issue because I'm encountering the error "Error: Memory allocation failed." when running the following dada2 command: `taxa
Hi Ben! I am using assignTaxonomy for trnL sequences with a custom database. We are currently working on getting the databse to work properly, so I used a test version...
Hello there, Can anyone explain me the below code, because when I try the final output says FALSE. Attached is the format of my csv file. I am interested to...
Dear all, I am a bit confused with the differences between two argument in the "filterAndTrim": 1. truncQ=2 2. minQ 3.The issue is that when I put minQ = 20...
Hello @benjjneb ! Hope you are well. I am currently running 2x300 PE samples on DADA2. Quality score looks good and doesn't drop below 30. Although, I observed an atypical...
We're just getting in our first standard 16S data from the PacBio Revio which is using the [Kinnex kit](https://www.pacb.com/technology/kinnex/), and will soon be getting 16S-ITS-23S data. I know the FASTQ...
So I am working on some AMPLICON sequences but we are having a problem with the quality of some of the DNA extractions mostly based on A260/A230 spec ratios. I...
Hi there, The Galaxy community maintains tool wrapper for [dada2](https://github.com/galaxyproject/tools-iuc/tree/main/tools/dada2) since quite some time and since recently also a [workflow](https://github.com/galaxyproject/iwc/tree/main/workflows/amplicon/dada2). Clearly a tutorial could increase visibility even more, e.g. in...
Hello, I´m working with some 16S v3-v4 sequences with Miseq 300pb, 200k reads per library. The sequencing service says they do not process de sequences for adapter removal. I checked...
Hi there! I'm working with bacteria and archaea 16S (MiSeq sequencing). More in specific I'm dealing now with the Archaea one (V3-V5) region. I was reading different issues (both open...
