dada2
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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
Hi! I have demultiplexed sequences for eukaryotes (18S) and bacteria (16S) in the same fasta file. I would like to analyze only the sequences for bacteria. I was wondering if...
I am using the DADA2 ITS (1.8) workflow to analyse my ITS data. I am running the cutadapt command on the reads and there is no output in the created...
I am a bit confused with the different versions of dada. The latest release on Github is 1.20 but bioconda and bioconductor offer a version 1.22. The output from `sessionInfo()`...
Hello, I have four fastq files named 18S191096-CZ_R1.fastq, 18S191096-CZ_R2.fastq, 18S191096-NEW_R1.fastq and 18S191096-NEW_R2.fastq. Also, the size of the 18S191096-CZ_R1.fastq, 18S191096-CZ_R2.fastq, 18S191096-NEW_R1.fastq and 18S191096-NEW_R2.fastq files is 227 MB, 227 MB,  2.5...
Where to start the DADA2, when your sequence are already quality filtered by the sequencing company?
Hi, I was looking at some sequences like- https://www.ebi.ac.uk/ena/browser/view/SRR13756225?show=reads Where there is one sequencing file from Illumina MiSeq, and in the published paper it mentioned that - The raw sequence...
Hi @benjjneb I have a new batch of sequenced samples that have been 16S sequenced using PacBio technology. I have two significant issues when processing the reads using DADA2 pipeline...
I am currently attempting to employ the dada2 ITS workflow for the removal of primers through a remote server HPC. The issue I run into comes from attempting to designate...
Hi, I have 40 samples split into 4 16s sequencing runs. But after merge the 4 runs and do alpha diversity analysis, I found they show significantly statistical difference from...
Dear developers, I am working with Illumina Miseq 300X2 data set of antibodies repertoires. the amplicons are > then 600 bp, in the mergePairs function I added `justConcatenate = TRUE`...
Hello @benjjneb and DADA2 community! I am having a very similar problem as issue #831 where I lose a considerable portion of my sequences during the merging step although I...
