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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
We are using DADA2 to infer alleles from MHC amplicon sequences. Basically we have hundreds of samples and need DADA2 to output fastas for each sample after merging and getting...
Hi Ben I have a pool of 24 samples (16S Pacbio) CCS reads. I wonder why I have such a difference of reads after the demultiplexing step between `lima` from...
Hello, I have a V3-V4 16s DNAr metabarcoding dataset of 68 samples with a read depth of 400-900K reads/sample. Samples were sequenced on a NovaSeq 6000 PE250. Primers were removed...
Hello: I'm trying to assign taxonomy with the MZGdb database, from [https://www.st.nmfs.noaa.gov/copepod/collaboration/metazoogene/atlas/index.html](url) particularly COI and 18s db. The data are offered in fasta, csv, morthur and psv format. Is there...
I am trimming primers and truncating using the filterAndTrim function and am finding that I have some reverse compliment primer left in the reads. I am working with V4 region...
Dear dada2 enthusiasts, Upon analyzing my HTS (Illumina Miseq 2x300bp) data generated after amplification of the CO1 I3-M11 fragment (ca. 396 bp without primers) I am faced with doubts about...
Hello, I apologise if I have missed this being discussed elsewhere but I couldn't find anything! I am following the DADA2 Pipeline Tutorial (1.16) and have not had any obvious...
Hi, I'm working with an 18S amplicon dataset sequenced on NovaSeq. On the error modelling step, learnErrors met convergence for both the forward and reverse reads, but the output graph...
Do you think I can generate a single-sample fasta file containing one sample id and all the sequences it involves from a seqtab.nochim? I mean, can I do it after...
Hello, I was hoping you might have some advice about understanding an issue I am running into with some microbiome samples (fungal community in soybean at ITS region). The issue...
