Can not detect spliced / unspliced counts

Question

[V]

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.

[ATpoint]

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

[V]

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.

[mubasher.mohammed]

Hi, did you manage to figure this out? Thanks

[V]

Yes, the whole bam file “possorted.bam” as outputted by cellranger needs to be remapped using RNA Velocity before importing into scVelo.

[mubasher.mohammed]

Thank you! That’s very helpful Is there any tutorial I can follow?

[V]

This should point you in the right direction. I would opt for the Python version of running it, and doing so on a cluster as most computers dont have enough processing power locally.

http://velocyto.org/

[mubasher.mohammed]

Thanks for sharing this, Very much appreciated info, Regards