PS: this message has also been cross posted on seqanswers. I just want to reach out to more bioinfo guys so thought of posting it here too.
So we have a dataset of variable biological insert library as we are sequencing the 5' and 3' end of transcripts. As a result the distance between the mates( <--- --->) is dependent on the length of transcript. To map the reads initially I am first using Mosaik which i belv does a better job with variable insert mate pair data.
After mapping we still see 40% orphaned reads where one read maps and the other doesn't. Is there a way that I can do a local re-alignment for these orphaned reads and attempt to map the mate within a given radius of the mapped mate.
Anything already out there ?