I am a newbie in analyzing single-cell data. I am working with single cell multiom ATAC seq data and I don't have the relevant single cell RNA Seq data. I have generated fastq files and count files using cellranger arc. As I don't have the sc RNA Seq data I used the same ATAC seq data (R1 and R2 fastq files) in place of scRNA fastq files to generate the count file using cellranger arc.
Now I am trying to use the filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz file to use the Seurat library in R. My goal is to find out cell type and generating the atacSeq UMAP like here https://satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html#wnn-analysis-of-10x-multiome-rna-atac
But I was able to generate the violin plot. But after that I get ridiculous error. Is it because I used ATAC Seq fastq files in the place of RNA seq files to generate filtered_feature_bc_matrix.h5 and atac_fragments.tsv.gz?
How can I generate something like this?
