How to add new coordinates to the existing .gtf annotation file

Question

[Santhi]

I have a few sequences that are not annotated in the reference genome. Using BLAST and STAR I was able to get the coordinates of all those sequences. Using IGV, I could visualize that my transcriptomic data has reads mapped to these coordinates. How can I quantify them?? Do I need to customize my gtf file? If yes, how can I do that?

Answer 1

[Trivas]

If it's just a couple regions, you can make a simple annotation file and use featureCounts. If it's anything more, you can make a separate GTF file and cat them together on the command line.