The fragment file exported by getGroupFragments() lacks reading support column

[Antidington]

Hi,

I'm working with fragment files exported by the getGroupFragments() function. When examining these files, I observed that they contain only four columns:

chr1    10043   10114   batch3_channel1_PB18#44_GGAAGTATCTCCTCTT-1
chr1    10066   10125   batch3_channel1_PB18#77_GTGAATCTCTCACAAA-1
chr1    10375   10437   batch3_channel1_PB18#37_CTAGCGGGTCCCGGAA-1
...

The files lack a read support column (column 5), which should indicate "the total number of read pairs associated with this fragment, including the read pair marked unique and all duplicate read pairs." according to 10X cellranger-atac count

Is there a way to modify the getGroupFragments() function to include the actual read support information in the output? Alternatively, is there another function or approach that preserves this important quantitative information when generating fragment files?

Thanks,
Jichen