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Hello,
I am using NFCORE_AMPLISEQ https://github.com/nf-core/ampliseq/tree/2.10.0, and it uses DADA2. I already posted this issue to https://github.com/nf-core/ampliseq/issues/764 and they metioned t…
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Hi all,
Just to start us off, I wanted to post something that I had gotten snagged up on when I first started using dada2 in R.
You need to use .fastq files and your .fastq.gz files should NOT…
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Hi,
I'm relatively new to bioinformatics and microbiology, and I've been following the DADA2 tutorial to process my 16S gDNA & eDNA sequencing data. After merging my paired reads and constructing …
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Hi,
I am having trouble with running Sequence quality control using DADA2 in `DADA2: 1.26.0 / Rcpp: 1.0.12 / RcppParallel: 5.1.6`
My script is as shown below:
`run_dada.R --input_directory /tmp…
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Hello All!
Im working with PacBio reads for the very first time. Compared to the tutorial, Im see im loosing really large number of reads. Below is the table:
Sample | ccs | primers | filtered…
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In the use of dada2 denoising of double end sequence, opened a screen background, there will be a mistake“An error was encountered while running DADA2 in R (return code 1), please inspect stdout and s…
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We have data across sequencing runs that we would like to merge together
dada2 has a method to do this: https://github.com/benjjneb/dada2/issues/716
Look at the format the datasets are in prior to m…
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I'm investigating biofilms living on plastic debris. I want to find out if there is differential expression of certain KEGG Orthologs (KO) at week 0 and week 7 of my microcosm experiment (as well as b…
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Hi,
I am using this pipeline to reanalyze some data from Illumina Novaseq PE250bp.
And I have noticed that in this paper , they sequenced at Hiseq PE250bp (McNichol, J., Berube, P., Biller, S.…
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Hi Shaun,
I have generated my own reference libraries for mulitple primers I am using. Details and the datasets (fasta formatted for dada2::assigntaxonomy and insect::learn, as well as the rds produ…