BEDPE format

The BEDPE format is specifically designed for keeping the alignment locations of each read pair from Paired-End library. This is not a general format but only a format for MACS3. It only contains three columns – the chromosome, the leftmost position of read pair, and the rightmost position of the read pair. All other information from alignment will not be kept in this format, such as the length of the read, the mismatches/gaps in the alignment, and etc. We can use this format to generate a simplified alignment file for PE library and gzip it to minimize the file size. An example is as followed:

chrXIII	0	60
chrXIII	1	64
chrXIII	1	211
chrXIII	2	46
chrXIII	3	154
chrXIII	3	209
chrXIII	9	71
chrXIII	11	67
chrXIII	11	71
chrXIII	14	71
...