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SnapATAC2 doesn't use the snap file format. It uses anndata format. SnapATAC2 can process BAM files with unlimited size as long as they can be stored on your hard drive. You can use this function to generate fragment files from bam files: https://kzhang.org/SnapATAC2/api/_autosummary/snapatac2.pp.make_fragment_file.html#snapatac2.pp.make_fragment_file, and then import them to create anndata objects using |
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Hello, when I creating snap files by using snaptools, I have met a problem. The bam file was too large (80G) and the program was killed for no reason. When I ran the program on a larger node (RAM 1T), I couldn't produce any valid results, which can be viewed in the H1930001_BS91_IC_002_ATAC_1.snap.qc file.
I found some similar questions before (r3fang/SnapTools#22). It said that spliting the bam file is a good way to solve this problem. I wonder if sanpatac2 still supports direct merging of different snap files.
And, more importantly, is it necessary to split bam files according to barcode? Or is it necessary to make the split bam file contain all the reads of the barcode under a certain number? Can I just split the bam file without considering the barcode information? Thank you.
Here 's H1930001_BS91_IC_002_ATAC_1.snap.qc:
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