Splice junctions in standard UCSC BED 6+3 format
Aligned by STAR

COLUMN 4: NAME: SJ<uniqueID>_A<Gencode 7 annotated=1 or not=0>_C<intron GT/AG=1 or not=0>_R1<=reads in replica 1>_R2<=reads in replica 2>
COLUMN 5: SCORE: 100*log2(ReadsRep1+ReadsRep2)
COLUMN 7: ReadsRep1+ReadsRep2
COLUMN 8: intuitive (non-parametric) IDR ("." when unpooled replicates)
COLUMN 9: Staggered ReadsRep1+ReadsRep2

dobin@cshl.edu