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Hi,
I'd like to use DADA2 to analyze my data from 16S and 18S amplicon sequencing. I've used bbduk to trim illumina adapters and then Mothur to make contigs and demultiplex. The problem is that I'v…
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I’ve a problem with my DADA2 output and I would like to seek your comment on this.
FYI, I’ve 2 samples with three replicates each, which all of them were samples of rhizosphere of the same plant, tr…
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I've been playing around with some amplicon data that came off a MiniSeq instrument, which apparently reports 8-level binned Q scores. Trying to understand whether we need to treat the filtering/trimm…
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Ciao,
I am using dada2 on PacBio sequences for the first time and I got a weird result after running the `makeSequenceTable` function. I got only 10,000 reads mapped to the detected ASVs (`sum(seqtab…
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when compiling swarm 3 with address sanitizer (see issue #120), a buffer-overflow is detected but it the error log is not very clear to me (see below). It could be an error in a shared-library.
```sh…
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We would like to discuss how best to correct richness/alpha diversity for differences in sequencing depth (total amplicons) when using the default dada2 pipeline, i.e. when using dada(, pooled = FALSE…
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Hi!
I'd like to try your approach to get a draft assembly for a 3kb amplicon. Most of the reads fully span the region with ~30x. Did you ever try this? It doesn't assemble a contig.
```
[17:40:19…
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I am a novice R-er and am probably making a simple mistake but I can't seem to find a description of this problem in other posts. I am working with a relatively large metagenomics data set that I succ…
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Hello,
I have a project where I have paralelly sequenced 16S and the functional gene bssA (for anaerobic toluene degradation) amplicons in various microbial communities. I am developing a workflow …
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IgBlast doesn't have a public bug ticket system (AFAIK) so I'm listing errors I've found here so people are aware of them. I will follow up with Jian @ NCBI about them.
I'm current testing with mou…