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Hello,
Do you have any advice for usage with [alevin](https://salmon.readthedocs.io/en/latest/alevin.html) output? Thank you
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
Alevin
**Describe the bug**
Maybe more of a support request than a bug.
I've got some of what I suspec…
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Hi,
I'm trying to simulate DropSeq reads. The paper for minnow says the user can specify the UMI and CB length but I can't seem to find an option for this.
Thanks,
Anna
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Dear Salmon Dev team,
I recently upgraded salmon 0.8.3 to 1.1.0.
I run the sample using libtype -IU.
For the new1.1.0, I used --validateMappings together with index built with genome decoys.
I not…
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Would it be possible to increase the authorised Hamming distance in the UMI collapsing step?
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Tried with latest version of `tximport` installed with `devtools::install_github("mikelove/tximport")` 1.13.3
```
tximport::tximport(file.path(alevin_dir, 'quants_mat.gz'), type = 'alevin')
Error…
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Hi,
I try to follow Alevin tutorial on 'How to Use alevin with Seurat' and have an issue with tximport(). I found this step is extremely **slow**. For **quants_mat.gz** file with **4.7M** in size, …
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[AD2.zip](https://github.com/csoneson/alevinQC/files/3284421/AD2.zip)
Hello,
I ran alevinqc_1.1.1 in R3.6 on the output files generated by Alevin-Salmon 0.14.0. I did not supply a whitelist to …
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**Is the bug primarily related to salmon (bulk mode) or alevin (single-cell mode)?**
salmon
**Describe the bug**
I used the default parameters to run salmon on mouse sample. But I got the warning:
…
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Hi,
I found the option of `--dumpUmiGraph` in `alevin` which, I suppose, gives the file to plot the UMI / Cell Barcode plot. However, after I run the analysis, I don't know how to extract that info…