I finished my GTF file, but now I am trying to use it in RNA-seq analysis to annotate the reads. The problem is that I merge 2 gtf obtained through different methods (Ensembl's reference genome, and a GTF created with Cufflinks from another RNA-seq). I am trying to merge the 2 gtf, but although the gene is only one, the exons are the same (and also the transcripts), being 2 isoforms with the same coordinates.
In this case, we have 2 genomes created with different methods that if the exons are the same, it probably means that they are the same exon.
I wanted the GTF to perform RNA-seq and annotate the reads. If two exons are overlapping, the HTSeq program will marked as ambiguous and won't count it as a valid read (look all the ambiguous counts).
__no_feature 454236 __ambiguous 2600391 __too_low_aQual 0 __not_aligned 335530 __alignment_not_unique 224705 3614862 not aligned 49608 aligned
Is there a tool that I can use to remove all overlapping transcripts?