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From the `alevin-fry` repo (by @fransua)
```
Hi,
I cannot find clear help on read_geometry. There are a couple of examples but they do not seem to work for me and I am struggling to change them.
…
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Dear community,
I have 4 lane files for each sample. I want to run Alevin on these samples. Alevin runs without any error, but the mapping rate is too low (about 5%). I tried different k-mers, diff…
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I noticed that inline code formatted text looks the same whether it's a link or just regular text. For example, these will have the same styling in `readthedocs` -
- [`SingleR`](https://bioconduct…
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Hello
I have some questions regarding the documentation in https://github.com/COMBINE-lab/alevin-fry#a-quick-start-run-through-on-sample-data
I read and worked through the quick-start and pull t…
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Closing #9 and #59, the previous issues on benchmarking preprocessing workflows, and opening a new issue to start discussing a concrete plan on building the tools we need for benchmarking.
In thin…
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Thanks for your work.
Everything works well with the demo testing data. However, when I have tested scRNAseq data from 10xgenomics 3' v2. Although the first part runs well. all reads were filtered ou…
LinAU updated
6 months ago
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Using salmon alevin v1.9.0, I noticed that my *total* reads were less than the deduplicated UMI count when I combined all three libraries together (from a NovaSeq run):
```
{
"total_reads": 2…
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### Description of feature
As per suggestion of @Zethson , it would be great to add a Mermaid graph to the readme to help users out who might want to do analysis of various types with the pipeline, e…
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Hi guys,
I was wondering if we plan to support various single-cell data analyses related packages within rust-bio or may be some sub-ecosystem ? As a starter, I've been writing very basic functions…
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Hello,
I tried creating a salmon index for bos taurus but was not successful. I created the decoy file using:
grep "^>" decoys.txt
sed -i.bak -e 's/>//g' decoys.txt
When i try to index usin…