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Dear kb_python Team,
As always - loving your aligner! However, I'm trying to run something slightly more unusual this time, and am having trouble getting the parameters right. I'm hoping that you ca…
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**Describe the issue**
I am running the latest version of kb_python to reproduce the example pipeline in the BIVI paper (which was using an older version of kb_python). I generated the loom successf…
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Hello!
Thanks for developing and supporting kb_python!
**Describe the issue**
I'm running [this](https://bustools.github.io/BUS_notebooks_R/velocity.html) workflow with [inDrops3](https://singlec…
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Add a note in the README specifying that, in case a meta colored dBG is built with the `partition` tool, the ref-ids in the pseudoalignment output are those returned by the `print-filenames` tool and …
jermp updated
9 months ago
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PSMFC mussel byssus project: I pseudo-aligned the tag-seq reads to the transcriptome and got 29.8% of the reads to pseudo align. Matt and I were wondering what the best way forward might be to increas…
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raw Manila clam reads on Gannet /var/services/homes/charlie/Manila_clam_egg_reads/raw. Note: the sample ID of "T" (treatment) and "C" (control) is mislabled for clam 193. It is a control clam. …
sr320 updated
4 months ago
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**Describe the issue**
When passing a custom technology string to `kb count`, it is incorrectly inferring a barcode length of zero. The command below is for SlideSeq data, but I have also tested this…
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**Describe the bug**
When executing ZARP on the mouse sarcopenia dataset to be described as a use case in the manuscript, the following errors are produced:
```console
InputFunctionException in…
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@shedurkin - To try to keep things a bit "cleaner", I've created a separate issue (originally taken from here: https://github.com/RobertsLab/resources/issues/1793#issuecomment-1920023835).
Code:
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kubu4 updated
9 months ago
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Currently the input channel for TxQuantSalmon and TxQuantKallisto tx_quant_inputs is built from [untrimmed fastq](https://github.com/LieberInstitute/SPEAQeasy/blob/master/main.nf#L874-L878).
I sugge…