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Currently, we use Nextclade to translate from nucleotides to amino acids.
We also use it to realign the notes and amino acids, even though our nucleotides are already aligned.
This seemed fine f…
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Hey,
I am trying to figure out some of the problems in your .sh script and might end up rewriting the pipeline using snakemake, would be very helpful to get the test .fna file that gives the output y…
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I'm trying vcztools on a zarr store that was not created with bio2zarr. This zarr includes an additional dimension 'nucleotides' which I would like to exclude from the output VCF but would rather nod …
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Hello,
There is a well characterized CAG repeat in the ATXN3 gene (exon 10). The latest variant catalog does not have that. Could you please tell me whether it is advisable to add the entire exon (…
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Is there an option in miRge to trim off nucleotides that are repeated more than `k` times? e.g. `ACGT[A* >= k]TGCA` gets trimmed to `ACGTTGCA`. I know this can be done prior to running the miRge pipel…
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Dear Torsten,
I want to calculate genetic distances between sequences that contain ambiguous bases, i.e. W, S, Y and so on. If I am not mistaken snp-dists can either ignore these positions or count…
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**Steps to Reproduce**
1. Launch “Ketcher” and switch to the Macromolecules module
2. Click on the “Open” button
3. Click on the “Paste from clipboard” button
4. Select the “Sequence” option and …
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Moreover, the cryo-EM map revealed the presence of an additional 13 nucleotides that were not previously annotated as part of the 28S rRNA (Supplementary Fig. 6).
https://doi.org/10.1038/s41467-024…
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Hi,
First of all, thank you for developing such an excellent tool! I am encountering an issue during the `windowmasker `step while processing my target genome. The error message I receive is:
``…
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**Describe the bug**
I am tracking the ith nucleotide of a DNA strand with 2 approaches that, I thought, should give identical results.
1) I generate trajectory.dat and browse through the file wit…