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Heya,
I have two runs (rep1, rep2) of 16S amplicon sequencing for 40 samples. The samples in 'rep1' are named like '1062-1-sampleNo1.R1.fastq' through '1062-1-sampleNo40.R1.fastq' and '1062-1-sample…
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Hello,
I am trying to validate a primer scheme and I get a keyerror message, see below:
```
(olivar) cygnus@pop-os:/media/extra_drive1/XXXX_tiled_amplicon_assay/olivar_v1.1.3_XXXX_scheme_developm…
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When processing ONT reads, iVar shifts the position of the read for reverse mapped reads. This results in incorrect alignment of the reads with the reference assembly. iVar seems to only change the po…
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I am creating a workflow that has many steps that use different tools, and I'm creating [minimal Docker images](https://github.com/Niema-Docker) for each of the tools. I was wondering which of the fol…
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Hi everyone,
Can I use this workflow for tumor only variant calling to detect both Somatic and Germline variants? Or should I first run my data with Mutect in tumor only mode and then use varlocira…
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Hi @benjjneb
To assign the taxonomy of v4 sequences, I use 2 consecutive steps according to dada2 tutorials:
`taxa
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Hello Community,
I am writing to seek your expertise regarding an unexpected issue I encountered while attempting to generate Prime Editing results. I meticulously followed the CRISPRESSO manual an…
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Hello @benjjneb,
Thanks for dada2 we are following your ITS pipeline, but are having issues with some unexpected read loss. We find ourselves losing a large majority of our fungal reads and we are …
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Keep the list of mutations and original copying node for every sample as qc metadata. It gets too hard reasoning about this after the fact, when layers of tree building are place on top.
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Hi,
I am trying to reproduce the DADA2 output of the extreme data set mentioned in _DADA2: High-resolution sample inference from Illumina amplicon data, 2016_ . I obtained the data set using the acce…