StringTie merge- can someone help me understand its output?

[BioLion]

Hello,

I am currently using StringTie merge on a StringTie output in order to discover genes that are not already in my reference annotation. I tried looking at the documentation but it is not very clear to me how to distinguish some things in the output or how it proceeds.

The command I have been using is :

${stringtie} --merge -G reference.gtf -o genome.StringTie.merged.gtf -F 1 -l GenomeX GenomeX.StringTie.sorted.gtf

with GenomeX.StringTie.sorted.gtf the output of stringTie.

I do not exactly understand how it works: when it finds a region which maps or overlaps, does it replace the line from "GenomeX..." by the line from "reference.gtf"?
Also, what is the difference with this command?

${stringtie} --merge -o genome.StringTie.merged.gtf -F 1 -l GenomeX listGenomes.gtf

with listGenomes.gtf being:
"reference.gtf
GenomeX.StringTie.sorted.gtf"

When I looked at the output of the second command, I did not see how we can distinguish between "reference.gtf" lines and "GenomeX.StringTie.sorted.gtf", or which field I am supposed to look at. Is there a way to do so after a merge?Also, does it choose between the two files when a region is similar?


Thanks a lot for reading me,

BioLion