GeneActivity without Fragments file in Seurat for Integrating scRNA-seq and scATAC-seq
Entering edit mode
8 months ago
el24 ▴ 40

Hi all,

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!

ATAC Fragments GeneActivity RNA Seurat • 656 views
Entering edit mode
10 weeks ago
Min • 0

Did you solve this problem? I am also struggled in creating ChromatinAssay object without fragment files......


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