Strand 0 in splice junctions table

[Smitha Shankar]

Hi, 

There are 3 values for Column 4 in the SJ.out.tab file- 0, 1 and 2.

Column 4 gives the strand information, I understand a value of 1 is on the positive strand and 2 is the negative strand, why are some junctions have strand 0?

Smitha

[Alexander Dobin]

Hi Smitha,

the strand of the junctions in SJ.out.tab is defined as follows.

1. For annotations (sjdb) junctions, it's assumed to agree with the strand of the transcript from which the junction originated. Note that some transcript may not have a +/- strand assigned, this is one  way you can get 0 

2. For unannotated junctions (or if sjdb is not used at all), the strand is defined by the intron motif: GT/AG, GC/AG and AT/AC are assigned +(1), and their reverse complementary -(2). The other (non-canonical) motifs are assigned undefined - "0" strand.

Note, that even if you have strand-specific data, STAR will not use this information to determined strand of the splice junctions.

Cheers

Alex