Why cufflink gives two transcripts/isoforms for one particular ORF ??

Question

[Chirag Parsania]

HI,

Follow this link to see the image. In that red annotation track refers to reference annotation while blue refers to assembly generated by cufflink. My doubt is though in reference annotation (orf.19 5465) is only one gene why cufflink has created two different transcripts with two different TCON ids (TCONS_00003972 and TCONS_00003973)

I have many of this in my data.

Kindly help.!

Chirag

[fta.mirzadeh]

have you run cufflinks with -g /*.gtf option?