Entering edit mode
7.7 years ago
ancient_learner
▴
680
Hi There seems to be a problem with bedtools pairtobed command. I have used the following command to check whether both ends in my bedpe file overlap with bed file. my bedpe file contains 6 columns (chr,start1,end1, chr,start2,end2).However I am surprised to see the output
pairToBed -a bedpe_file -b bed_file -type both
chr10 14400000 14440000 chr10 22040000 22080000 chr10 14400000 18240000
where 1-6 columns are from my bedpe file.
