I have a RNA-seq dataset. I used
Cufflinks to align to my reference genome and make an assembly of my transcripts driven by a
GTF of my genome.
I have an interest gene (9 exons), I am looking if it is expressed in my data. When I look at it in the assembly, I found it split in 2 parts. The 3 first exons in a transcript. And the 6 last exons in another transcript. I was thinking that the expression level was too low to make a good assembly of this transcript. But when I look at the sashimiplot from the
.bam file used for the assembly, here is what I have:
I have enough reads supporting the junction, but
cufflinks reports 2 transcripts.
Any idea about why is this happening?
EDIT: Could it be comming from my parameters?
-u --min-frags-per-transfrag 10 --max-multiread-fraction 0.99 --trim-3-avgcov-thresh 5 --trim-3-dropoff-frac=0.1 --overlap-radius 50