dada2
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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
Environment specifications: R version 4.3.2 (2023-10-31) -- "Eye Holes" Linux OS: "Rocky Linux 8.9 (Green Obsidian)" packageVersion dada2 1.30.0 Hello, I am processing sequencing reads downloaded from Short Reads Archives....
Hello, I am gettimg error during the process of assign taxonomy. I am working on COI genes and trying to use Midori2 database. The percentage of nochim was low in...
Hello, I'm working with some illumina 16s V3V4 sequences, and I'm not sure how can I improve the non chimeric sequences. I have used the next for filter and trim...
Hi! I'm working on 16S sequences from Illumina 2x300, with targeting regions V3-V4 (341F-785R)... Forward: Reverse: These are the quality profile after cutadapt. We were trying to target the lenght...
Hi there, I’m double checking/proofreading a DADA2 workflow script that was initially run in January of 2022 to make sure everything is still working fine. I am running the script...
I have samples sequenced targeting the same 16S partial region from two different institutions, with about 120 and 300 samples respectively. I'm unsure how to correct for batch effects, so...
Hello Dr. Callahan, As per the instructions, I downloaded the SILVA database (training set) and placed them in the directory containing the fastq files. Ran the command line: taxa
Hello, im encountering a similar issue to related to my sample reads. After completing the Dada2 pipeline according to the tutorial, i created a phyloseq object, but in doing so...
Hi, I am looking at some data from the 2 x 150 bp V4 region, and when I look at the quality plot, we see a drop in the middle...
Hello. I was analysing the error rates of my filtered files and I got some strange plots that don't fit perfectly for some base transitions. Should I proceed, if not,...
