Strand Fusions

[MP]

I'm trying to understand the strand of fusion obtaining from star. I use total stranded RNA so  I  expect to have my fusion with a direction of + and + and -
ad Star give the alignment respect of + strand.
Why I found this type of fusions:
POSTN--USP14    5    0    INCL_NON_REF_SPLICE    POSTN^ENSG00000133110.10    chr13:38138664:-    USP14^EN
SG00000101557.10    chr18:204648:+    M02898:39:000000000-AH4BK:1:1107:10766:11431,M02898:39:000000000-AH4BK:1:2119:17
989:25191,M02898:39:000000000-AH4BK:1:2116:22047:22310,M02898:39:000000000-AH4BK:1:1116:21878:16115,M02898:39:000000000-
AH4BK:1:1107:12395:9910    .   

So means the 5' is in antisense (the left gene) and the right gene on sense? Am I right?
I found in you script this notes.

What is the law in this? Could you please explain me?

 # two options, depending on sense or antisense alignment (antisense orientation just a consequence of DS trans assembly)
   
    #          L                               R
    #        ------> gt...................ag -------->             
    #
    #   |=================>              |==================>
    #         gene A                            gene B
    #
    #        <------ ......................<---------
    #           R                               L
    #
    #  if left:
    #      can be donor matching sense of geneA
    #      can be acceptor matching antisense of geneB
    #  if right:
    #      can be acceptor for sense geneB
    #      can be donor matching antisesnse of geneA
    #
   

[Brian Haas]

The + and - designations should correspond to the genome orientation of the read alignment.  All fusions reported as mapped to genes should always be in the sense orientation with respect to the exons of the corresponding genes.

best,

~brian

On Wednesday, October 14, 2015 at 3:40:43 PM UTC-4, MP wrote:

I'm trying to understand the strand of fusion obtaining from star. I use total stranded RNA so  I  expect to have my fusion with a direction of + and + and -

ad Star give the aligntment respect of + strand.

[MP]

 In total stranded my 1st read is on the opposite strand of the RNA molecule while the other follow the rna molecule. ie. Rna molecule read1=- read2=+
My fusion could be A/B and B/A so I expect to have more B/A then A/B because my strand are follow that information!!
What do you think? Please could you explain more..