Can you pull out novel internal exons from TECtool?

[aleighbrown]

Less of an issue, more of a question ( which I could maybe solve myself by trying out the tool)

Can you extract novel internal exons as well as the novel terminal exons using TECtool?

Cheers and thanks,

AL

[fgypas]

Hi @aleighbrown

No, we focus only on novel terminal exons. For novel internal exons, I would recommend a tool like StringTie (https://github.com/gpertea/stringtie)

I hope this helps

Foivos

[aleighbrown]

Why would you recommend stringtie?

[fgypas]

For internal exons, it worked well for me in the past. You can also have a look at this paper: https://doi.org/10.1093/bioinformatics/btv488. Of course, new tools might be out there that could work better.