scATAC-seq and scRNA-seq integration issue

Question

[inayat45shaikh]

Hi All, I have scATAC-seq and scRNA-seq multi-OMICs dataset and I am trying to do integration analysis with the tutorial using vignette https://satijalab.org/seurat/articles/atacseq_integration_vignette.html But at co-embedding step when I am trying to visualize the integrated data, the plot seems not properly integrated (see below plot), as it labeled ATAC cells as “NA” in the UMAP.

Here is the detail of my data scRNA-seq: One cell line treated with four timepoints (DMSO, Treat1, Treat2, Treat3) scATAC-seq: One cell line treated with same above timepoints (DMSO, Treat1, Treat2, Treat3)

What do you think went wrong with the integration? I have pasted script below for your reference

[GenoMax]

Please do not repost the same question again in a new thread. Ref old thread- scATAC-seq and scRNA-seq integration issue

This question will likely be deleted.

While it is natural to feel impatient to receive help/answers, people who provide that help here are doing so for free and on their own time. So you need to be patient.

[inayat45shaikh]

Thanks GenoMax, Mistakenly added. I tried deleting the other one, but couldnt find any tab to delete.

Best Inayat