Applying XClone to mouse scRNA-seq: xclone.pp.xclonedata

[NickolasTeo]

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

[Rongtingting]

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]

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]

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