Hi every one! I've been using tuxedo pipeline for RNAseq analysis and now I'm stock with cummRbund. I've used a reference annotation.gtf in my tophat and cufflinks runs. in this annotation my gene of interest has only two isoforms but when I try to visualize expression bar plots for isoforms using cummRbund it result in to 3 variants. its weired because when I load my annotation.gtf to IGV I can clearly see that there are only 2 transcripts for my gene. trying to understand a little more I view isoforms cuffFeature of my gene using cummrbund annotation function and saw that one of isoforms is repeated twice but with different length.
I've asked this question in bioconductor support but nothing came up. any help on why this is happening or how to fix it is appreciated
