dada2
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benjjneb
Accurate sample inference from amplicon data with single nucleotide resolution
Hi Ben, I'm working on jellyfish microbiome and recently performed a primers comparison trying to find the best primers for me. I noticed that for what seems to be the...
@benjjneb Hi, I used to manipulate MiSeq reads on Qiime2 where I can use DADA2 plugins along with other q2-plugins easily. I need to export the sequence data as fasta...
Dear Dr Callahan, I hope this message finds you well. Thanks a lot for all the work and development you have done with this package. It is very useful for...
# dada2 pipeline for metabarcoding (CO1) Thanks a lot for your dada2 pipeline, this is really cool. Our research group has been using it for our human microbiome projects. This...
I am working with 16S data sequenced on a Miniseq instrument and I am having difficulty interpreting these error plots where the fitted model drops off at higher quality scores....
Hi Ben, My code has been working perfectly but I have, since I visited it last month, been having issues getting it to work Today I got a new message...
I'm having trouble with handoff to MaAsLin2 (https://huttenhower.sph.harvard.edu/maaslin/). It seems to be an issue with my taxa table. Does anyone have a script or suggestions to fix this? Thanks very...
Hello, I am a novice when it comes to R so excuse this basic question. I have been following the dada2 pipeline and have created the seqtab.nochim after pair merging...
Hello Benjamin, I sequenced the V3-V4 region of 96 stools samples (2x 250b) with the degenerate and closely related primers: FWD 341: CAACCTACGGGNGGCWGCAG ACCCTACGGGNGGCWGCAG TCCTACGGGNGGCWGCAG CCTACGGGNGGCWGCAG REV 805: CATGACTACHVGGGTATCTAATCC ACGACTACHVGGGTATCTAATCC...
Hello!! My name is Edgar, I am a new user of dada2 and microbiome analysis in general. I have a question about the tricked out value of R1 and R2...
