Different no of 'unknown/class u' transcripts in merged.gtf and final.gtf files

Question

[SKY]

Hello!

1.Can anyone explain why the no of 'unknown/class u' transcripts in merged.gtf and final.gtf files/sample are not same?

2.Does that mean that final.gtf files are itself a subset of merged.gtf ?

3.If i take a union of all tmap files {made from final.gtfs} + remove duplicates, I will end up with same number of transctips as reported by tmap file {made from merged.gtf}?

Any help please?

Thank you Akash