Analysis of single-cell dataset that includes both single- and paired-end samples?

[zhang-jiankun]

Hi @kaizhang,

Thank you so much for developing such a great tool! I'm working on a single-cell ATAC dataset that includes both single-end and paired-end samples. Could I do analysis by following Multi-sample Pipeline: analyzing snATAC-seq data of human colon samples? Is there anything crucial we need to be aware of?

Best,

Jiankun

[kaizhang]

SnapATAC2 will not work if you want to import both single-end and paired-end reads from one experiment (i.e. from one fragment file) to a single AnnData object. But it should work if you want to use different AnnData objects (paired-end or single-end) to create AnnDataSet. Nothing in particular needs to be taken care of except to be aware of potential batch effects as a result of sequencing technology differences. Let me know if there is any issues.

[zhang-jiankun]

Thank you so much, Kai! Sorry for my delayed response. I've been doing data preprocessing and cell clustering, and SnapATAC2 performed very well. However, I’m facing an issue with creating a gene matrix using the AnnDataSet object. Do you have any suggestions? The SnapATAC2 I am using is 2.5.3.