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Dear Dr. Benjamin,
I have been reading the DADA2 article of yours published in Nature methods. I am working on a microbiome project in which I need to compare microbiome (16S amplicon) data from two …
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Hi,
I tried mixcr 4.1.0, but the issue in #811 still exists. Mixcr still kept printing "writing clones : 100%", but no alignments or clones were written into the .clna file.
I ran the assemble comma…
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- [x] Aligned reads
- [x] Total reads
- [ ] Chromosome coverage
- [ ] Coverage across reference
**Aligned reads and Aligned percentage**
Data is in [`genome_results.txt`](https://github.com/ewels/Mul…
ewels updated
2 years ago
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hej,
I was wondering if there is (did I miss it?) - or if you plan to add - the possibility to construct a phylogeny within the DADA2 pipeline? I was thinking something like Fasttree.
Along that li…
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For the [datasets in the DDE](https://data-staging.niaid.nih.gov/portal/wip/?from=1&filters=includedInDataCatalog.name%3A%28%22Data+Discovery+Engine%22%29&q=), I get different answers than what's in t…
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I've been incorporating CoDA-valid methodologies in my workflows ever since I realized the caveats of using relative abundance. There's not many packages that implement CoDA versions of differential e…
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Hello,
I have run ShapeMapper2 to calculate map data for two 1500-nt overlapping amplicons. During library preparation they were fragmented, so not all obtained reads contain the sequence of amplic…
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Hi all, I've been working on understanding why my average coverage has been lower after switching to basecalling using bonito v031 models. I am curious if other users are seeing the same issue. This i…
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Hi,
here the session info:
> library(breakaway)
> library(phyloseq)
> library(magrittr)
Warning message:
package ‘magrittr’ was built under R version 4.1.3
> library(tidyverse)
-- Attac…
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Currently, we are using two separate files to indicate our primers:
- `reference/primers.fasta`: This is used by BBDuk in the `TRIM_PRIMERS` step. We can generate this using the [`getfasta` command…