I am attempting to combine Single-end (SE) and Paired-end (PE) ATAC-seq samples into a single AnnDataSet for downstream analysis using snapatac2. The Problem is SE samples store fragment information in adata.obsm['fragment_single'] while PE samples store fragment information in adata.obsm['fragment_paired']. When these are combined into an AnnDataSet, the disparate keys in .obsm lead to issues where downstream functions cannot locate the fragment data because they expect a consistent key across all underlying AnnData objects.
What is the best practice for joint analysis of mixed-end libraries in SnapATAC2? Is there a recommended way to "standardize" these keys before merging (e.g., treating PE as SE) without losing data integrity? Does AnnDataSet support mapping these two different keys to a universal fragment interface?
Thank you for your help!
I am attempting to combine Single-end (SE) and Paired-end (PE) ATAC-seq samples into a single AnnDataSet for downstream analysis using snapatac2. The Problem is SE samples store fragment information in adata.obsm['fragment_single'] while PE samples store fragment information in adata.obsm['fragment_paired']. When these are combined into an AnnDataSet, the disparate keys in .obsm lead to issues where downstream functions cannot locate the fragment data because they expect a consistent key across all underlying AnnData objects.
What is the best practice for joint analysis of mixed-end libraries in SnapATAC2? Is there a recommended way to "standardize" these keys before merging (e.g., treating PE as SE) without losing data integrity? Does AnnDataSet support mapping these two different keys to a universal fragment interface?
Thank you for your help!