Vignettes for 10x Multiome data? about liger HOT 4 CLOSED

Hi Tan,

Thank you for trying out LIGER. At the moment, LIGER doesn't support integrating single-cell multimodal data (e.g. 10x Multiome).

These bed files are not outputs from the cell ranger, and you could generate them yourself (e.g. in R). They are essentially the coordinates of each gene/promoter. There are a few related discussions (genes: https://www.biostars.org/p/427912/ , promoters: https://www.biostars.org/p/8207/).

Best,

from liger.

Thank you @cgao90 very much for the prompt help and detailed reply! It's super informative.

Best,
Tan

from liger.

Hi LIGER team,

Do you by any chance have the hg38 promoter and gene bed files?

Thank you!
Jenny

from liger.

Hi @jshi7 ,

Here are two example hg38 promoter and gene bed files you can try (https://www.dropbox.com/sh/tkky33qd6fu6a4n/AAAVsSDYJZJj2vqu0J1UsVmya?dl=0). MT genes are not included.

Best,
Chao

from liger.