Merging different gtf files

[TluckDucky]

Hello,

I'm very new to transcriptomics and I'm struggling a lil bit when using GffCompare/GffRead to merge gtf files.

I built a human transcriptome using taco and removed some transcripts class codes (= , e k, m, n, p, s) after using the gffcompare utility.

Now, I need to merge my assembled transcriptome with the GENCODE's transcriptome (adding from the reference, the removed classes from the assembled transcriptome), removing redundant transcripts but I can't figure out which options to use.

I used the following command:

gffread --merge gencode.v41.primary_assembly.annotation.gtf newTrasncriptome.gtf -o mergedTranscriptome.gtf

Could you please give me any tips?

Thanks in advance.