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Looking at the modified base tags section there are a limited number of modified bases found in the specifications page. At nanopore we are working on a number of other modified bases and wondering wh…
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According to the current definition, a "Sequence Collection" is "a **set** of reference sequences", however, I believe that in order to be useful, this should be changed to an "**ordered set** of refe…
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Dear devs. The GFF v3 produced by the pipeline does not include STOP codons in the coordinates of the CDS and fails parsing (or shows wrong) by some downstream tools and genome browsers. I am guess…
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We need to begin adding functional annotation information to the genome browsers. The most straightforward way to do this is via the annotation gff3 file, prior to creating the apollo/jbrowse files. …
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We need to confirm the final contents of the string to digest. Right now, I think we had settled on these elements:
## contents
- name (*e.g.* `chr1`)
- length
- topology
- sequence digest (re…
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Hello, I am trying to use GCsnap to analyze a clustered .clan file that I prepared using MMseq2 and clan from MPI bioinformatics toolkit. The example test worked fine, but now I get stuck on step 2: F…
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Hello, I have run into an issue accessing your lab's data from the recent TOGA paper at this URL: https://genome.senckenberg.de/download/TOGA/. I am suddenly getting a 403-Forbidden error, but I had n…
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```bash
results/intermediate/
|-- host.fa.fai
|-- host.fa.gz
`-- map-to-remove
```
has these files. But when I `gunzip` the `host.fa.gz` I can not load it into IGV.
![image](https://github…
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Bactrocera cucurbitae has been changed to Zeugodacus cucurbitae. We'll need to:
- create new directories with the new species abbreviation on all servers that are symlinks to baccuc
- Update tripa…
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In this page:
https://www.pombase.org/status/new-and-removed-genes
Use the data from this autogenerated table from the genome_changelog repo.
https://github.com/pombase/genome_changelog/blob/…