How to use numbat in other species with a phased genome?

kharchenkolab / numbat

Haplotype-aware CNV analysis from single-cell RNA-seq

https://kharchenkolab.github.io/numbat/

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How to use numbat in other species with a phased genome? #174

Open xinghua1001 opened 6 months ago

xinghua1001 commented 6 months ago

Hi, Thanks for developing this smart tool. I am currently working in a species with a phased genome, which can easily provide haplotype information. We also have enough population genotype data. In this case, is it possible to use Numbat for single cell CNV analysis?

Thank you!

teng-gao commented 5 months ago

Hi, no need to use population phasing if you have fully phased genome for an individual. See the mouse tutorial

xinghua1001 commented 5 months ago

Thanks for reply! In the run_numbat() function, the genome parameter is limited to (hg38, hg19, or mm10). Can we set it to Null?

teng-gao commented 5 months ago

Hmm, currently there're only three genomes with gtf dataframes that come with the package (e.g. gtf_mm10). Adding a note here to allow users to provide custom GTF in the future. For now you may have to hack the code to achieve this ..