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Hi, I am running a set of samples through DADA2 pipeline and I found an unusually high number of Rev comp primer hits. In my previous experience, the Rev Comp hits are generally low (~1k-2k). May you …
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Hello,
I try to analyze paired 16S rRNA reads from prokaryotes, which I extracted from metagenome data (sequenced on Illumina NextSeq) using SortMeRNA. The metagenome reads have been trimmed (read …
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Hi,
I am working on amplicon sequencing data with UMI.
After grouping with GroupReadsByUmi (strategy=identity), among others UMI families I get the two below(showing a couple of the reads) :
UM…
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Hi @benjjneb,
For my amplicon sequencing analysis usually I use DADA2 stand alone or Qiime2 based DADA2. Recently, I came across LotuS2 (https://lotus2.earlham.ac.uk) bioinformatics pipeline which …
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Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer's Disease and Obesity -- Zhang et al. -- Frontiers in Immunology
https://www.ncbi.nlm.nih.go…
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Hi, I'm still relatively new to R and I'm struggling to get my files to demultiplex.
path
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Hello!
I tried now several times running "learnErrors" of DADA2 in R. Loading the package worked fine and every step described until that. It runs about an hour, gives as output "**5485896480 total…
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Hi there,
I got a bulk rna-seq data of T cells with 10X Single Cell Mouse TCR Amplification Kit. Although it's a weird way to build the library, I still would like to do the analysis. Since the l…
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As we run the assign taxanomy and add species command. but the result contain only NA in species column
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Hi, this is my first time using Dada2 to work with ITS. I sequenced the ITS1-1F region using 2 x 250 bp, so I have a lot of variation in the amplicon size. I followed the ITS workflow so far (https://…