Error in GetAssay.Seurat - RNA is not an assay present in the given object

[mairamirza]

Hi everyone,

I am trying to convert my Seurat object to H5ad, but I keep running into an error when I try to save the file. My object has both the RNA and SCT assays, yet it’s still not working.

MuDataSeurat::WriteH5AD(seu, 'ko_counts.h5ad', assay="SCT")

Error in GetAssay.Seurat(object, assay) :
RNA is not an assay present in the given object. Available assays are: SCT

Here is a quick summary of my object:

seu
An object of class Seurat
47739 features across 31313 samples within 2 assays
Active assay: SCT (23232 features, 3000 variable features)
2 layers present: counts, data
1 other assay present: RNA
4 dimensional reductions calculated: combined_pca, umap, harmony, umap_harmony

and my session info:

R version 4.3.3 (2024-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0

locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

time zone: Europe/Berlin
tzcode source: system (glibc)

attached base packages:
[1] stats graphics grDevices utils datasets methods base

other attached packages:
[1] MuDataSeurat_0.0.0.9000 stringr_1.5.1 SeuratDisk_0.0.0.9021 SeuratObject_5.0.2 Seurat_4.3.0.1

Anyone know how I can fix this? Would really appreciate any help!

Thanks in advance!