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Hi,
Thank you for developing this useful tool. I just came across the paper in Nature Communications; congratulations! My lab develops the `alevin` tool, which is currently supported in `single…
rob-p updated
2 years ago
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
Alevin single-cell mode.
**Describe the bug**
Hi, I bumped into a problem following this tutorial [https://com…
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Hi,
I was skimming through some of the code and other open issues on support for other library (cell barcode/umi) designs. It looks like there is code for supporting inDrop libraries, but I wasn't su…
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### Description of feature
I'm following up on a slack post that I put out 2 months ago at https://nfcore.slack.com/archives/CHN5BV5DW/p1712178056321859
I had a question about the fastq format nee…
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### Description of feature
I am using the alevin-fry quantitation method. For downstream analysis, I am mainly interested in the final count matrix, e.g.
1. The content of the `af_quant/alevin di…
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Hi everyone,
Is there a way to feed pre-transformed files into Alevin? We've been using Valentine's nice umis repository https://github.com/vals/umis as our preprocessing step to put sample, cell a…
roryk updated
5 years ago
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
Alevin
**Describe the bug**
`Wrong barcode-end parameters`
`[2019-01-17 15:50:10.269] [jointLog] [error] wron…
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Hi,
Is there an option in Alevin to allow for some mismatching? I'm working with some relatively poor quality data mentioned in #258. Both STAR and Alevin report alignment rates around 45% for this…
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According to https://github.com/COMBINE-lab/salmon/issues/434#issuecomment-540533728 the current behaviour of the Alevin wrapper in which each fastq file provided in a collection is analysed separatel…
pcm32 updated
4 years ago
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Hello,
I am doing single nuclei RNA seq and have issues with cellranger discarding lots of reads and would like to directly compare between optimizing the cellranger reference to deal with overlaps e…