how to convert h5Seurat to h5ad for large object

mojaveazure / seurat-disk

Interfaces for HDF5-based Single Cell File Formats

https://mojaveazure.github.io/seurat-disk

GNU General Public License v3.0

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how to convert h5Seurat to h5ad for large object #99

Open FADHLyemen opened 2 years ago

FADHLyemen commented 2 years ago

Hi, I am trying to convet large h5Seurat file into h5ad, BUT can not allocate the memory for this big file. Any help?

library(Seurat)
library(SeuratDisk)
library(SeuratData)
kpmp_blue=hfile <- Connect("xx.h5Seurat")
kpmp_blue_Seurat=as.Seurat(kpmp_blue,slot = "counts", assay = "RNA")

every time it killed in HPC with 200 GB ram, any suggestions, my h5Seurat file is 11 GB.