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Hi, I would like to use the scrnaseq pipeline to generate the TCC matrix output (transcript-compatibility counts) from kallisto-bustools. (I am trying to generate the cell x transcripts matrix instea…
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Hello,
I am facing a rather strange issue while running kb count. I am using the workflow=nac and it runs perfectly for my other set of fastq files. But for this one, it produced similar error but …
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Hello,
Thank you for keeping kallisto alive. These days, more and more I realise how its actually important and hard maintain and update tools across many years.
# Background:
I am processing …
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Hi,
I have been following this tutorial on generating spliced and unspliced matrices for RNA velocity analysis: https://bustools.github.io/BUS_notebooks_R/velocity.html#generate_spliced_and_unsplic…
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Tutorial: https://www.kallistobus.tools/velocity_tutorial.html
The sticking point is getting introns programmatically from every possible GTF. I've had success with [gffutils.FeatureDB.create_intro…
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Hi,
I have been following this tutorial on generating spliced and unspliced matrices for RNA velocity analysis: https://bustools.github.io/BUS_notebooks_R/velocity.html#generate_spliced_and_unsplic…
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Users will often have their own internal retina scRNA data and would like to compare their data directly to the scEiaD dataset without having to:
- Download the huge amount of data to reprocess
…
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In the barcode parsing code in bustools correct
https://github.com/BUStools/bustools/blob/master/src/bustools_correct.cpp#L711
it supports barcode files of the format
```
AAAA GGGG TTTT
- TTTT…
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I am interested to run slingshot trajectory using your guideline using my Seurat object (Normalized, PCA, tSNE, UMAP, clustering done)
https://bustools.github.io/BUS_notebooks_R/slingshot.html
>…
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Hello,
I keep getting this runtime error when using kb count to generate unspliced and spliced count arrays. Note that I used kb ref previously to generate the necessary files using the genome.fa a…