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single-cell-genetics / XClone

Detection of allele-specific subclonal copy number alterations from single-cell transcriptomic data.
https://xclone-cnv.readthedocs.io/en/latest/
Apache License 2.0
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Applying XClone to mouse scRNA-seq: xclone.pp.xclonedata #10

Open NickolasTeo opened 10 months ago

NickolasTeo commented 10 months ago

xclone.pp.xclonedata currently only supports hg38 and hg19. Can you please also support mm10 for the RDR analysis of mouse scRNA-seq

Rongtingting commented 10 months ago

Hi Nicklolas,

I have extended the XClone to mouse dataset by updating xclone.pp.xclonedata. You can have a try by specifying the genome_mode as mm10_genes.

I recommend you use xcltk to do the preprocessing, the gene region file you used in xcltk RDR is also provided, annotate_genes_mm10. You may need delete the header before you used this file in xcltk.

hxj5 commented 10 months ago

I updated the gene annotation file "annotate_genes_mm10" above to make it compatible with xcltk basefc -r. The new annotation file is in dir preprocess_mouse/data. See xcltk RDR part for full parameters of xcltk basefc.

NickolasTeo commented 10 months ago

Thanks, xcltk works now, but had to rename the annotate_genes_mm10 file to tsv instead of txt. I'll write back if there's any issues with XClone