FAQs

How to proceed from 10x cellranger-atac output bam file?

We provided a module convert10xbam, which convert 10x cellranger-atac style position sorted bam file to scATAC-pro style bam file. scATAC-pro -s conver10xbam -i 10x_positionsort.bam -o output, it will output bam of scATAC-pro style in output/mapping_result/, and mapping qc stats and fragment.bed file in output/summary/.