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Hello,
I am using Clair3 for variant calling on amplicon sequencing data from a minION, generally with a fair amount of success. However, for one particular amplicon, I get a large number of false ne…
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Is there a way to make a .fna file and .biom file after using the DADA2 pipeline in order to run PICRUST2 as described below:
The standard pipeline will generate metagenome predictions for 16S rRNA…
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I have an issue with successfully running the genebe commandline tool.
**input command:**
`genebe annotate --input 24072-01-01_split.vcf --output 24072-01-01_split_genebe.vcf --progress`
**erro…
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I wanted to run some checks to see if I could identify the variants produced by DADA2 in my input files. I mapped my original PE amplicon fastq files to a high quality species-specific reference genom…
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I did ITS sequencing of stool samples for Fungi. However when I look at relative abundances, even for phylum 60-70% of my relative abundance graph is Other DNA.
When I look at how my ASVs map with…
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I have five plant nrITS amplicon sequence files (~650bp sequence length) from five plant leaves (PacBio 0.999 CCS reads) with 1189 reads (combined) and 95% of them are singletons.
The sequence qual…
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I'm working with samples and having issues at the merge step (I'm losing ~75% of my reads at that step). I want to look at some denoised read pairs to see if I can identify the problem. If I have the …
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Hello!
After the remove chimeras step in DADA2 v1.2, I'm getting the following errors in my log output. Any help would be greatly appreciated!
```
abundance forward reverse nmatch nmismat…
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Hi folks,
I am using wf-amplicon to extract consensus sequences which may align to one of many references. The report is very useful in that I can see which reference sequences are present in my sa…
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## Major enhancements
### Included strand-bias annotation for ivar
NGS data are prone to certain types of artifact variant calls, strand bias is a clear example. For example, all but one variant…