Here’s a program for converting bed file to junctions. can be cloned from Github.
usage ./bin/bedToJunction <filename>|<stdin>
suggested usage: bamtobed -i <bamfile> -cigar | ./bin/bedToJunction - > junction.bed
**** use <-> when using stdin
Needed a bed file with cigar string
output file contains six columns:
column 1: chromosome name
column 2: junction start position (0-base start pos)
column 3: junction end position (0-base start pos)
column 4: name (ordered by chrom)
column 5: number of reads supporting
column 6: strand [+/-]