Hi,

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
<p>The insert size it specified by the aligner and for RNAseq where the paired-ends don&#39;t overlap or when they span a splicing event or other type of junction (e.g., fusion bounds), these may be unreliable. The end position of the mate isn&#39;t stored in the BAM format, so you need to find the mate and then get its end. I&#39;m not familiar with the Bamtools API, so I can&#39;t say whether it provides a convenient method for this or not, though I wouldn&#39;t be surprised if it doesn&#39;t.</p>
