If I only have the 10x matrix files for scATAC and don't have the fragments file, can I use Signac to analyze the scATAC data? How should I do it?

[szbssg]

When I wanted to analyze the scATAC data from GSE169246, I found that the authors only provided the mtx files and did not provide the fragments file. I encountered many difficulties during the analysis. I would like to ask if it is possible to generate a fragments file from the 10xATAC mtx files, or how should I proceed with the analysis?

[timoast]

You cannot generate a fragment file from the matrix. You can read about the fragment file format here: https://www.10xgenomics.com/support/software/cell-ranger-arc/latest/analysis/fragments-file

[Jyoung-0108]

哈喽，你找到解决办法了吗？我也想分析这个数据集，发现没有fragments文件

[szbssg]

没有那个文件就没辙

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