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zhanghao-njmu / SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.
https://zhanghao-njmu.github.io/SCP/
GNU General Public License v3.0
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RunSCVELO #109

Closed namorosini closed 1 year ago

namorosini commented 1 year ago

Hi, I'm trying to run the SCVelo but I'm facing the following error:

Error:SystemExit: None

How can I fix that?

Thanks!

zhanghao-njmu commented 1 year ago

Do you have spliced and unspliced assays in your Seurat object? If not, you need to generate and add them to your Seurat object using velocyto.

namorosini commented 1 year ago

Thank you so much! It worked!

qindan2008 commented 1 year ago

RunPAGA with pancreas_sub occurred error:

Error in t.default(adata$layers[[k]]) : argument is not a matrix

image
zhanghao-njmu commented 1 year ago

The error is caused by using base::t instead of Matrix::t, as base::t does not support transposing sparse matrices. SCP has already ensured that it internally calls Matrix::t since a long time ago, so please make sure that you are using the latest version of SCP. @qindan2008

denvercal1234GitHub commented 1 year ago

Hi @zhanghao-njmu @namorosini, I was able to convert my concatenated looms of different samples into 1 in Python and converted that to Seurat object. Would you mind helping me to add the spliced and unsliced (and any other info needed) from my loom-converted Seurat object to my GEX Seurat object in R? And, do I need to normalise or anything with these counts? In the typical scVelo pipeline there is normalisation before computing velocities.

Thanks so much!