input formats for validPairs

[QianzhaoJ]

Hi
Very useful tools for differential analysis of Hi-C data !
I found that the input file should be a name-sorted BAM file, and I used the pipeline HiC-Pro to generate the final bam files, can I use it for the input file in diffhic ? And I found that I need to assign and filtering fragments in diffhic , so maybe I can use the ValidPairs file in HiC-Pro as input files ?
Thanks in advance !
Best wishes
Qianzhao

[LTLA]

It should be possible to use any name-sorted BAM file in preparePairs(), so if HiC-Pro produces that, then you should be good to go. All other formats will probably just confuse diffHic. I haven't personally had time (or, TBH, interest) to write import functions for other Hi-C formats, but you may be interested in some discussions here.