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I am applying CNVkit to targeted amplicon sequencing data by following your command:
cnvkit.py batch -m amplicon -t targets.bed *.bam
Is this command using the default bin size of 200?
Some of …
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nextera transposases cannot insert at the extreme ends of amplicons. To handle these libraries, it would be necessary to enable partial matches with expected start sequences.
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See this as a workflow:
```
Building OTUs, would require that your reads align very nicely. That is pretty hard with Nanopore reads, and you end up with a lot of singletons. I have tried clusterin…
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**Describe the bug**
When running the following cmd, `CRISPRessoAggregate --prefix tmp/CRISPResso_on_BNL17517_additional_80k --prefix tmp/CRISPResso_on_BNL17517_additional_80k-160k --name "80k"` erro…
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Hello,
Firstly, thanks for an interesting paper to read this morning!
I usually work with Nanopore data in a metabarcoding context, and was wondering if you have any idea how effective S-conLSH…
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Dear author:
I am running AA many times, but the execution always stuck at "Plotting SV View"
Besides, the summary.txt shown that " #Amplicons = 8 "
But my results always cannot save image when …
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Dear Benjamin, apologies if this is not a real "issue", but I am curious to know why dada2 tutorials (such as 1.2 tutorial but i think others as well) explicitly state that they asume you are working …
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[mydata.zip](https://github.com/erasmus-center-for-biomics/Nimbus/files/2285517/mydata.zip)
I used Nimbus to analyze my data, with a bed file and pair end fastq data, using the hg38 reference.
I…
booew updated
5 years ago
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Hello,
Thanks for this very useful package!
I just have a few questions after runnning on single-cell ATAC-Seq libraries generated from the 10X multiome kit. I ran using the following commands:
…
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Hello,
Thanks to develop this fantastic pipeline.
I'm looking forward to reading your paper!
I have amplicons from a nanopore metabarcoding run that did not span 16S rRNA gene but another gene.
I…