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YaqiangCao / cLoops

Accurate and flexible loops calling tool for 3D genomic data.
https://yaqiangcao.github.io/cLoops/
MIT License
109 stars 17 forks source link

Strand information #2

Closed ozturan closed 6 years ago

ozturan commented 6 years ago

Hi,

I just wanted ask a quick question about the strand information. Is it required to specify the strand in the input .bedpe file? Or is it enough to provide chr1-start1-end1-chr2-start2-end2-score?

Thank you.

Dogancan

YaqiangCao commented 6 years ago

Please added the strand info and other information as required by BEDPE in our readme. The strand info was used to estimate a auto EPS for ChIA-PET data. And for HiChIP, actually not affect the result. So if you actually don't have the strand info, you can make it up as + or -. For example as following: 'chr19\t270000\t275000\tchr19\t280000\t285000\t13\t.\t+\t+\n'