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Hello,
Thank you for this great tool!
I'm working with amplicon sequencing data capturing SMN gene. However, my data demonstrate uneven coverage along the SMN1 gene, which has resulted in question…
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The workflow requires paired-end data, but we may be able to use just the first read (when the Illumina adapter are ligated on the PCR amplicon product in random orientation).
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associated with: http://ivory.idyll.org/blog/2017-sourmash-sra-microbial-wgs.html
see https://github.com/dib-lab/soursigs/blob/3db6162579e0efbc4fe8f181a7f08c3aee391d97/Snakefile#L149
```
http:/…
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Hey Martin!
I ntoiced a weird occurrence when running covid-truth-eval on artic assemblies built from simulated read sets, whereby a true SNP in the VCF of the artic assembly is incorrectly being i…
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@antgonza when downloading wastewater studies with amplicon data, almost all of them are coming back ambiguous even when it's clear from the study page that it is 16S, e.g. https://www.ebi.ac.uk/ena/b…
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### Checklist
- [X] I added a descriptive title
- [X] I searched open reports and couldn't find a duplicate
### What happened?
```
(base) daniel@LAPTOP-RIGEUJL3:~$ conda env create -n qiime…
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After merging the reads and checking for the V3LOOP amplicon, check for T-cell receptor alpha and beta (TCA and TCB) matches. Take all of those matches, and report the most common nucleotide sequences…
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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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We have a subset of 60 samples from [Karthikeyan et al.](https://doi.org/10.1038/s41586-022-05049-6) that show a transition between delta and omicron variants.
To run it live in a workshop we need t…
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Hello again!
I want to process the sequencing data obtained by Croce _et al_ in **"Phage display profiling of CDR3β loops enables machine learning predictions of NY-ESO-1 specific TCRs"** with TRUS…