Split RNA Seq reads

Question

[vaishali.chakraborty91]

Hi,

I have run RNA alignment for paired end data with split/chimeric alignment enabled - one of the split read of Mate-1, I noticed is aligning to the same exon but in the middle of the exon. Example representation:

............--------split-segment1------------................---------split-segment2-------------

============================                                                                                         Exon-10 of Transcript-1
=======================================================================   Exon-10 of Transcript-2

Can a split read align at the middle of an exon? Is it possible or it should align only at the exon boundaries?

Thank you,

Vaishali

[GenoMax]

Is there just one read or you have multiple reads supporting that observation. This may also be some library prep artifact.

[i.sudbery]

Or alternatively, if there is plenty of support (many, non-duplicate reads), then your probably looking at a novel unannotated splice junciton.

[vaishali.chakraborty91]

Thank you i.sudbery and genomax for the responses. Only one read is behaving like this.