I'm currently using BamTools to parse a (paired-end) RNA-seq bam file for detecting possible chimera.
I'm focusing on reads where both pairs belong to different genes but I have a hard time to understand some of the BamTools::BamAlignment members.
For example, it is easy to get the starting position of the mate read using the "al.MateRefId" for the chromosome and "al.MatePosition" for the coordinate but I still lack its end position. For standard reads (both pairs belonging to the same gene) I can get the mate end-position using "al.Position + al.InsertSize" but is it still true for chimeric reads? If not, how is InsertSize computed and how can I get this mate end-position?
Many Thanks in advance