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Hi,
I want to detect chimeras on 16S nanopore data, similar to [this post](https://github.com/natir/yacrd/issues/52) I've tried vsearch now, but as vsearch was developed for high quality short read…
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Hi,
I am aware that it is recommended that "raw" data is used as input for ANCOM and ANCOMBC. In the context of amplicon data it is clear that this means count data that has not been normalised for…
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Hi!
Apologies if this is answered elsewhere and I didn't find it. I was wondering if you could confirm that I am using CNVKit appropriately:
I have a cohort of all-male WGS samples tumor and no…
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It's unclear why there is a hard coded sequencing run and other details in the amplicon processing, see https://github.com/qiita-spots/qp-knight-lab-processing/blob/8696401a3aa4bdce6135b5a66e6186af8da…
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Following up on our conversation from earlier, you mentioned it would be nice to program in a graceful fail when there are no sequences that pass the primer check in ngsfilter. I decided to run eDNAFl…
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Hi,
I am using Clair3 on targeted amplicon sequencing data and our amplicon can have duplications and/or deletions. Is there a way to especify polyploid variant calling so that the program looks for …
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Hi,
I am using Clair3 for variant calling on targeted amplicon sequencing data. Since we are using the R10 flowcell and the model provided by ONT was trained at 60x depth, we subsample the bam to 60x…
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Currently for `augur ancestral` we have:
```
--keep-ambiguous do not infer nucleotides at ambiguous (N) sites on tip
sequences (leave as N). Always true for VCF inp…
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Hi everyone,
I have an issue with the CRISPResso analysis of some of my NGS samples (Input: paired end fastq files, amplicon sequence and gRNA added).
The goal is to see the editing efficiency…
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Hi,
I tried to demultiplex at once both R1 and R2 files but then after checking that R2 barcodes are NOT in the *UNKNOWN* files it turned out they are. It seems `demultiplex` throws the who read -p…