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I'm looking for clarification on the Skipper config file. Some terms really confused me.
Does the "STAR_DIR" refer to the STAR index folder?
Could you provide an example for the "REPEAT_TABLE…
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It seems the analysis strongly depends on the annotation files provided in config.yaml. In the readme, the origin of some of the annotation files is vague. I would appreciate clarification on the fo…
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The overall idea is to allow toggling between the 'cells' view (umap/tsne) with a 'genes' view (heatmap probably) so that cellxgene users can get a sense of the overall shape of the dataset from a gen…
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I am trying to sort and index the `.gam` file. The command line I used is
```
vg gamsort -p -t 16 x.gam -i x.gam.sorted.gai > x.sorted.gam
```
I got an error after running 17 hours.
```
break …
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HiCUP does not give nice output if HTML summary reports are not generated owing to lack of Tidyverse, Plotly and/or Pandoc. Make this more elegant.
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Pretzel has asynchronous loading and display of requested blocks, which provides a more responsive user experience.
Extending this to load fractional parts of blocks will be necessary for the larger …
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---
#### Comments with open items :
- :construction: [2022Jun17](https://github.com/plantinformatics/pretzel/issues/317#issuecomment-1158270210) (Don-Isdale)
- [2022Aug01](https://github.com/p…
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Up until now we've basically preserved exactly what is in the GFF3 that is imported, with only a bit of formatting changes to store it internally. However, this has led to some places in our code that…
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New error when running taxonomy
**Command:**
cd $tmp
in_dir=/projects/cmi_proj/blood_microbiome/niaid/combined
out_root=$in_dir/shogun
align_dir=$out_root/wol_alignments
taxonomy=/projects/c…
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## User story
>As a website user
>I want to be able to access the files that I previously had access to on the CNGB server
>So that I can still download them if required
## Acceptance criter…