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I've been trying to use fastx_collapser to collapse a CDS fasta file to unique sequences only (so I can build a kallisto index with it). However, I've been getting the persitent error:
"fastx_colla…
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Hi @drneavin,
This isn't really an issue, I was just wondering if you have run Demuxafy using the outs from other UMI calling tools like alevin-fry or UMI tools? If one uses a tool that employs pseud…
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**Describe the issue**
kb count of 1.6B 10X reads runs for days (run not completed yet) on a 16-thread computer. Based on my previous experience and the run time statement in your preprint, the run s…
dsb66 updated
5 months ago
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**Describe the issue**
Thank you for creating such a wonderful tool! I would like to ask you about the difference between `adata.h5ad` and `cells_x_genes.total.mtx`. I ran `kb count` and used an outp…
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Hi team KB,
We are trying to use **kb count** with a new **10x Visium** dataset (https://www.10xgenomics.com/resources/datasets/visium-cytassist-mouse-embryo-11-mm-capture-area-ffpe-2-standard) whi…
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Hi
I have been trying for 3 days but still coulnd't get it work on my end. Sorry I have very little knowledge and training in bioinformatics so please bear with me with the basics. I had RNA-seq da…
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[Cross-posting](https://github.com/pachterlab/kallistobustools/issues/58) from kallistobustools repo because I realized this repo has more activity:
I've run into an issue with running CSP data (T…
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Here, I found a question, please ask everyone, is Error: kallisto index file not found index.idx_cdna.
Detailed description:
kb count --h5ad -i index.idx_cdna,index.idx_intron.0,index.idx_intron.1…
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Reproduction:
- Repeat steps here https://github.com/algbio/themisto/issues/28#issue-1868676686 but remove the newline at the end of the last line, or remove more lines, for example being left with
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I am trying to quantify RNA reads from SlideSeqV2 data using a custom technology string (-x ) and a kallisto index (_version 0.50.1_) with help of the kb count (_kb_python 0.28.2_) command. The total …