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Dear salmon team and @k3yavi,
I am an happy user of alevin on scRNAseq data (10x). In some circumstances, I have to compare samples from very uneven sequencing depth (less than 100k reads per cell …
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### Description of feature
Universc is currently broken (it likely was for a while, because tests were running with the `-stub` option).
Prerequisite to make it work would be to finalize the modu…
grst updated
4 months ago
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Hello!
This might be an unusual request, but I have been attempting to use Salmon Alevin for mapping of **scATAC-seq data** (10X Genomics platform) and have a few questions on how to best do this (/w…
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### Name of the tool
STAR (STARsolo)
### Tool homepage
https://github.com/alexdobin/STAR/blob/master/docs/STARsolo.md
### Tool description
The single-cell / demultiplexing version of ST…
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Hello salmon team! @jamorrison and I were looking through the code and seeing how best we could contribute a new single-cell RNA-seq technology. Our approach (STORM-seq https://www.biorxiv.org/content…
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hi!
while this has been discussed in detail in #379 , there have been many releases of Alevin since then.
So i am just a bit confused, if i want to generate a quant matrix of all CBs including tho…
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I am running alevin on the 10X V3 pbmc 1k data set and I am getting a strange warning when running the following command:
```
salmon alevin -i salmon-index/ -p 16 -l IU --chromiumV3 -1 pbmc_1k_v3_fa…
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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
3 months ago
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Hello! I’m using alevin-fry to map and quantify single nuclei RNAseq data. I’m trying to merge technical replicates but need to use separate permit lists (each generated from a provided list of valid …