Hi all friends,

For an RNA-seq analysis, I used STAR for mapping reads on the genome followed by Stringtie for genome-guided assembly. I downloaded a GTF file of my interested organism from Ensemble and merged it with annotation file produced by Stringtie. For getting tss_id and p_id required for cuffdiff analysis, I used cuffdiff_gtf_attributes script here, on the merged annotation file produced by StringTie, but just tss_id was added. However, when I tried the script on the original GTF file, both tss_id and p_id were added. Could you please let me know what's wrong with merged GTF file and why the only tss_id was added to it?

In your professional opinion, if I should again do the RNA-seq analysis from read mapping with the original GTF file that tss_id and p_id were added to it? Hope there is a better solution instead of running again the whole analysis, I haven't much time.

Thanks