dada2
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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
Hello, first of all thank you for all your very useful replies from different posts. I work with 16S datasets from different sequencing experiments using different primer sets and would...
Hi Drs, I tried to use this software to run learnErrors. I have been running for three or four days with no results, how can I solve it? reads.in reads.out...
I am trying to run 16S reads on dada2 but I can not get my reads to merge. I just get this message. > mergers
I have problems intalling DADA2 in the latest version of R 4.1 Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.1 (2021-08-10) Installation paths not writeable, unable to update packages path: C:/Program...
Hi I am trying to assign taxonomy for my V3-V4 sequencing following your tutorial https://benjjneb.github.io/dada2/tutorial.html. While using silva_nr99_v138.1_wSpecies_train_set.fa.gz database resulted more species assignment than using silva_nr99_v138.1_train_set.fa.gz followed by silva_species_assignment_v138.1.fa.gz. Issue...
Hi everyone, I actually have the same question as [alices0701] had on 16 Aug 2019; https://github.com/benjjneb/dada2/issues/829. I'm not very good at working in R so I could really use a...
Hi, I am using the DADA2 outputs tutorial to analyze my data and I am having issue with the merging step. The commands that I used are listed below: #...
Please can anyone tell me why i kept on getting FALSE for this command identical(colnames(ASVs),rownames(taxa)). identical(colnames(ASVs),rownames(taxa))i tried checking the ASV counts and Taxonomy counts, they are both the same number...
We are doing a combined analysis of samples, where few samples were sequenced on Hiseq platform with paired end reads for V4 region of 16S rRNA and another group was...
At least for dada2=1.22.0, `mergePairs()` returns a list if there is > 1 sample, but it returns as data.frame if there is only one sample. This inconsistent return can cause...
