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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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allvalidpairs to bedpe format #362

Closed KunFang93 closed 4 years ago

KunFang93 commented 4 years ago

Hi, Nservant

I was wondering if there is a way to convert allvalidpairs results to bedpe format like this 

chr1   9945 10095   chr1      248946216 248946366   .   .   +   +

I found that in this thread, you mentioned that 3rd and 6th cols is the middle of the reads. So I guess this conversion will be good? 

chrom    3rd-(read-len)/2    3rd+(read-len)/2  chrom    6th-(read-len)/2    6th+(read-len)/2  .   .   strand1    strand2

Thanks! Best, Kun

nservant commented 4 years ago

Hi Kun, Yes, it should be ok. Of note, the position which is in the allvalidpairs files are now the 5' of the reads. In the first HiC-Pro versions, I was indeed using the middle of the reads, but this has been change in the latest versions. Best

KunFang93 commented 4 years ago

Understand~Thanks for your reply!

Best, Kun