Comments (4)
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.
Related Issues (20)
- How to transfer cell labels from one dataset to another dataset? HOT 2
- Missing value OptimizeALS HOT 4
- Error in Integrating multiomics RNA and ATAC data after removing one cell-type from RNAseq data HOT 3
- Integrate multiomics RNA and ATAC data generates trivial all-zero latent values HOT 3
- Genes and promoters information for Mouse species HOT 2
- How to split sample of function (plotByDatasetAndCluster) HOT 2
- recovering expression for differential analysis HOT 6
- getProportionMito() is currently mouse-specific HOT 1
- mergeH5 function - error #000: ../../src/hdf5-1.12.1/src/H5L.c in H5Lexists(): line 943: unable to get link info HOT 2
- Unable to use unshared arguments using LIGER v1.0.0.0 HOT 1
- Add option for Leiden algorithm HOT 1
- plotgeneloadings, runGSEA, plotWordClouds error
- Subsetting integrated seurat object and reclustering using liger HOT 1
- Integrating SCTransform-normalised data with LIGER HOT 1
- problem with read10X and createLiger HOT 3
- Lowest suggested value for lambda? HOT 1
- "shared factor neighborhood" not used anymore as described in the paper? HOT 3
- log transform data first? HOT 1
- Another request for help regarding SCTransform HOT 1
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