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This ticket emerges from HTAN-446: https://sagebionetworks.jira.com/browse/HTAN-446
> Our bulkRNA seq data consists of FASTQ level 1 files (for which there is an existing assay, no issues there) an…
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As discussed at length in #159 , the current default GRCh38 genome (iGenome) confusingly uses the NCBI reference, whereas other genomes use Ensembl by default (e.g. GRCh37, GRCm38).
This configurat…
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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…
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Hi,
I encountered another issue after my first issue #133 was successfully solved.
Im working in a conda environment generated as follows:
```
mamba create -n af -y -c bioconda -c conda-forge sim…
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**Describe the issue**
Our lab is performing single nucleus analysis, I am trying to use Kallisto to pre-processing our data for RNA velosity analysis. My pipline is stucked at kb count step.
kb v…
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Hello,
I'm trying to run kallisto quant with the pseudobam option, and it is consistently running into a segfault error. Do you have suggestions on debugging that I could try? Below is the command …
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I am testing our usual quantification pipelines with `kallisto` and `bustools`, and noticed `bustools capture` seems to have problem with its barcode mode, if the barcodes are long (in this case, 38bp…
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Hi kb-python team,
I am interested in processing some published Smart-seq3 data to get unspliced and spliced counts (mainly out of curiosity).
This was the command I tried to run with `kb count`…
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Hi,
I have an experiment wih a whitelist composed of 35 barcodes (60bp long, non standard technology in development) and when I try to run bustools correct I immediately obtain :
(/bioinfo/local…
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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
8 months ago