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bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data
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Cell Ranger weight valuse error #11

Open Qtasnim opened 3 years ago

Qtasnim commented 3 years ago

Hi !

I used Cell Ranger pipeline v 4.0.0 for my clustering analysis, and no weight columns were generated in the Cell Ranger file. Although it says it's backward compatible, I cannot seem to be able to run my file and "Cluster 1 Weight column not in the input table!" Error message appears.

Do you happen to have a v 4.0.0 supporting code?

Thank you.

bioinfo-ibms-pumc commented 3 years ago

I'm sorry for the inconvinence. Could you please send me your input file for the title lines? I'll check it. I just tested SCSA for the input file from https://support.10xgenomics.com/single-cell-gene-expression/datasets/4.0.0/Parent_NGSC3_DI_PBMC?, and found that it could be work well with v4.0.0 format. Thanks!

Qtasnim commented 3 years ago

Hello...

Thank you for the reply. I have tried the data set included here and it worked perfectly. I would be very thankful if you could check it for me, if possible.

Graph-Based Genes.txt

Thanks a lot

bioinfo-ibms-pumc commented 3 years ago

Hi, Qtasnim. It seems like that the title of your file is not consistent with Cellranger's official header. Because SCSA uses pandas to read the expression, so the header is very sensitive for the process. The simplest solution is just replacing the title header from the data you tested above and remain the cluster number information.