I'm not certain what's the best way to do this, so any help will be highly appreciated.
I have a merged gtf file that I created after doing rna-seq>
stringtie pipeline with a refernce genome.
I also have other gtfs and files such as:
RFAM DB results,
exonerate (protein alignment) result, ab initio result from
I then used the
transdecoder tool to predict ORFs but I only used the stringtie merged gtf file.
Is it better to try and merge all of my diferent inputs to get a larger and more descriptive gtf and then use
transdecoder on it for the final results, or should I use
transdecoder on the rnaseq pipeline resuls and then merge the result gff with the other gtfs I got from different type of evidences?
The goal is to create gene prediction models based on all this evidence and the input genome.
Thanks a lot.