I am new to R and Seurat, and I am following Seurat tutorials to find anchors between RNA-seq and ATAC-seq data according to:
Combining the two tutorials is difficult for a cell line data set I am using for SNARE-seq Human here.
I managed to run the following code and get PCA and UMAP for both RNA-seq and ATAC-seq data, but when I run the following code I get an error:
gene.activities <- GeneActivity(atac, features = VariableFeatures(rna))
Error in GeneActivity(atac, features = VariableFeatures(rna)) : The requested assay is not a ChromatinAssay.
I am struggling to create a chromatin assay using the following code in the second tutorial because the fragments file (fragments structure) is not available in this dataset, I only have TSV matrix format of cells x genes (or peak regions in ATAC-seq)
chrom_assay <- CreateChromatinAssay(
counts = atac_counts,
sep = c(":", "-"),
genome = 'hg38',
fragments = frag.file,
min.cells = 10,
annotation = annotations
I appreciate any solutions or workaround to fix this issue so that I can run the GeneActivity() function to identify anchors between RNAseq and ATACseq data. I have read tutorials on Seurat and Signac packages, but none helped me fix this issue.
p.n: In an article, I found sinto package is being used to create fragments files from bam files. I also found fastq files on SRA so I am creating fragments files.
Thank you very much!