Mbtools read-frequency outputs the total modification calls per every read in the Bam file.
The -r option filters for reads which intersect in regions provided by a bed file
If a read spans two of such regions, two entries are created in the output with identical read_names but can be distinguished by their start_position and end_position which indicates the partition of the read the modification calls are associated with.
Mbtools
read-frequencyoutputs the total modification calls per every read in the Bam file.The
-roption filters for reads which intersect in regions provided by abedfile If a read spans two of such regions, two entries are created in the output with identicalread_namesbut can be distinguished by theirstart_positionandend_positionwhich indicates the partition of the read the modification calls are associated with.