Question: Can not detect spliced / unspliced counts
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gravatar for V
7 days ago by
V230
UK/London
V230 wrote:

Hello,

I keep running into an error whenever trying to run an scVelo analysis, once my data is loaded (tried different formats, like mtx and csv), I get the error

WARNING: Could not find spliced / unspliced counts.

I have generated these files directly from the barcodes.tsv, genes.tsv, and matrix.mtx provided in the filtered output of the cellranger pipeline. Also tried it with the unfiltered ones and still getting the same error.

Would anyone be able to let me know if I'm missing something basic, or should I try to get these from somewhere else? CellRanger pipeline v 3.1.0 was run on transcriptome GRCh38-3.0.0

Thanks you for any info.

scvelo rna velocity rnaseq • 63 views
ADD COMMENTlink written 7 days ago by V230

We cannot read minds. Please add relevant code for preprocessing and running the tool.

ADD REPLYlink written 7 days ago by ATpoint34k

I literally only did :

adata = scv.read('matrix.mtx', cache=True)

After obviously importing all the necessary packages. The error above pops up after doing that.

The other consideration I had is that our genomics core uses the default (10xgenomics provided) GTF for GRCh38, and this does not seem to contain intronic regions. I'm assuming then they would need to be remapped? Would you have access to an intron containing GTF to remap.

ADD REPLYlink written 7 days ago by V230
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