FRAG format

This is an format for the fragment files defined by 10x genomics to store the alignments from single-cell ATAC-seq experiment. It can be regarded as the BEDPE format, containing the chromosome, the leftmost position of aligned fragment, and the rightmost position of the aligned fragment, with two extra columns – the barcode information and the counts of the fragments aligned to the same location with the same barcode. It is usually generated by the cellranger-atac or cellranger-arc pipeline. But this is a fairly straightforward format so one can easily convert other alignment results into this format. An example of the fragment file is like:

chr22   10768839        10769063        AAACGAAAGACTCGGA     2
chr22   11333072        11333249        AAACGAAAGACTCGGA     1
chr22   11363891        11364010        AAACGAAAGACTCGGA     1
...