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I'm thinking about trying this out for a backend for my VEBA eukaryotic binning module (https://github.com/jolespin/veba) as an alternative to MetaEuk.
Looking at the examples here:
```
Helixer.…
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Since we have mutations that are point sites or are more generally in certain domains or other large features of the protein. For example, MD Anderson creates these for each gene and they are customi…
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Hi,
Thanks for this super nice method and the pipeline. In the minimap2 bam outputs, I don't see any junction reads even though minimap2 is run with the `-x splice` parameter. Sashimi plots are all…
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Define SPARQL queries that can be used to answer the information needs described in the use case flash card and the mindmap linked from #57 by relying on the information models defined in the Virtual …
mroos updated
2 months ago
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**Have you checked the [list of proposed rules](https://github.com/Benjamin-Lee/deep-rules/issues?q=is%3Aissue+is%3Aopen+label%3Arule) to see if the rule has already been proposed?**
- [x] Yes
…
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Hi everyone
I have been working with the National Institute for Communicable Diseases (NICD) on some of their SARS-CoV-2 sequencing. I adapted the "variation" workflow to call variants in Illumina …
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I ran smoove annotate and got this error (below). But the smoove.square.anno.vcf.gz was generated. When I ran bcftools stats the anno file had 1 less record than the input vcf. Not sure what to make o…
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Hi,
I have run the FastSMC with T = 50. I want to calculate the DRC statistics for my dataset. Is there a script to calculate this statistics from the FastSMC output?
Thanks a lot!
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We should discuss how to best represent variants. Probably we need something flexible like
HGVS
NM_123:c.-123C>T
with various types that also work for chromosomes, microdeletions, and other sets of …
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CQ matrix is [here](https://docs.google.com/spreadsheets/d/1wbP1Ykryibcan2ZgZTOmnGp9WjcRE7nNig3akiq0PuY/edit?ts=5852eaf2#gid=19786600)
List of databases is [here](https://docs.google.com/spreadshee…