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kaizhang / SnapATAC2

Single-cell epigenomics analysis tools
https://kzhang.org/SnapATAC2/
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Analysis of single-cell dataset that includes both single- and paired-end samples? #250

Closed zhang-jiankun closed 4 months ago

zhang-jiankun commented 4 months ago

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 commented 4 months ago

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.