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FelixKrueger / SNPsplit

Allele-specific alignment sorting
http://felixkrueger.github.io/SNPsplit/
GNU General Public License v3.0
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How to phase Hi-C data using SNPs #63

Closed hmyh1202 closed 2 years ago

hmyh1202 commented 2 years ago

Hello:

In your wiki, Hi-C data must be produced by HICUP ?

How about HiCpro software ？

The Best . Thank you !

FelixKrueger commented 2 years ago

To be completely honest I don't know if it would work with HiCpro data. All I could find about the specific requirements for Hi-C was that R1 and R2 (the bait and prey/other end or whatever you want yo call it) follow each other on consecutive lines in the BAM file (see here: https://github.com/FelixKrueger/SNPsplit/blob/master/SNPsplit_User_Guide.md#hi-c-data). Maybe it is just worth a shot?

hmyh1202 commented 2 years ago

OK, fine, I will try it, thank you.