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