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I have a custom MultiQC module called `target_phasing`, which can be found [here](https://github.com/lumc/multiqc_pgx). It runs in MultiQC v1.11 and before, but not in MultiQC v1.12 or later. The modu…
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Hi,
I have toy sample with only one barcode, and I used kallisto bus to create gene matrix.
I want to create a plot of reads vs UMIs for each gene.
The out put is, obviously, already collapsed and …
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Whenever I run kallisto bus with 10xv1, I'm getting "Segmentation Fault: 11" with no further detail. Any advice?
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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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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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I have installed the following packages already:
pcaMethods
hdf5r
However...when I use the code: install_github("velocyto-team/velocyto.R")
I receive the error:
clang: warning: no such sysroot …
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Great tool that integrates lots of functions!
I was wondering if there is a way to get the isoform counts. I was trying to get the isoform counts following your Nature paper (specifically https://g…
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I am trying to re-process the [data from Grun et al 2016](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM2142263) (a CEL-Seq paper), and I am getting very low counts from kallisto and bustools,…
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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 …
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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…