TopHat Junctions visualization help

[adrian]

Hi:

I need some help in interpreting Junctions.bed in a browser.

I have 4 different junction.bed files from 4 different samples. I uploaded them in IGV (Broad) and I see the transcripts. File attached.


For instance in NUPR1 gene, all 4 junction files have trascripts that overlap CCDC101 and IL27 genes.

1. Why are transcripts starting in CCDC101 gene and ending in IL27. Is this because of novel TSS for CCDC101 and novel TES.

2. What is the meaning of <> and << between exons?
it is my understanding that < or > denotes direction + or - ve of Transcription. then what does <> and << or >> denote?

Thanks for your help.

Adrian

http://img864.imageshack.us/i/nupr1.jpg/

Image reference is posted in new message. Sorry for duplication.