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:

isoform_id     gene_id CDS_id gene_short_name TSS_group_id class_code nearest_ref_id                  locus length
1 TCONS_00047384 XLOC_021135     NA       NR_026816     TSS26199          =      NR_026816 chr6:31132113-31154094    593
2 TCONS_00047385 XLOC_021135     NA        LC050987     TSS26200          j       LC050987 chr6:31132113-31154094    885
3 TCONS_00047386 XLOC_021135     NA        LC050987     TSS26200          =       LC050987 chr6:31132113-31154094   1369
  coverage     gene_id class_code nearest_ref_id    gene_short_name                  locus length coverage
1       NA XLOC_021135       <NA>           <NA> LC050987,NR_026816 chr6:31132113-31154094     NA       NA
2       NA XLOC_021135       <NA>           <NA> LC050987,NR_026816 chr6:31132113-31154094     NA       NA
3       NA XLOC_021135       <NA>           <NA> LC050987,NR_026816 chr6:31132113-31154094     NA       NA

any help on why this is happening or how to fix it is appreciated.