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I'm running the pydna.Assembly a number of times. I notice that when I execute my code, I get anywhere from 4-7 different assemblies, depending on the run (just running the same code over and over aga…
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Im analyzing Structural variations using Pysam. The structural variations are a result of the dna being sequence is circularized. Meaning when i map it back to the reference genome i get a lot of soft…
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Hello,
I am running Canu in a High Performance Computing cluster.
I used Canu for a bacterial genome assembly (draft) successfully.
I am trying to assemble another genome, but the job has failed…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```python
3.6.3 (default, Oct 17 2017, 14:49:00)
[GCC 4.9.2]
CPython
Linux-3.16.…
ghost updated
5 years ago
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Hi Florent,
I am trying to run your pipeline with 9 genomes.
I didn't externally prepared annotation files, to just rely on Pantagruel's built-in annotation.
Here is how my input directory/files…
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In the context menu of a feature, allow the user either to export the feature as a GenBank file, or to copy the feature to clipboard in the GenBank format (JBEI said either option would be fine)
**…
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The default plotDendro is limited to only 6 discrete values. I tris to run the dna_plotDendro(clust,....) coord_flip() program but I got this warning message
Warning messages:
1: The shape palette…
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Hi there and thanks for maintaining the library.
Since version 1.71 and pull request #1497, FeatureLocation will throw an error if its ``end`` parameter is lower than it's ``start``. The problem i…
Zulko updated
5 years ago
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This proposal suggests to use the ComponentDefinition.type field in order to express whether DNA (RNA) is circular or linear and double stranded or single stranded. In contrast to the alternative prop…
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Hi,
I am trying to run taiyaki on the data provided in the walkthrough for modified base detection. I installed taiyaki in a virtual environment (taiyaki 4.1.0, torch 1.1.0, numpy 1.16.3).
When ru…
fneuh updated
5 years ago