I have a question regarding the merging of genomic annotation files. I am annotating the genome of a plant, and for practical reasons, I decided to perform the annotation on each chromosome individually. I used Braker3. At the end of the annotation process, I obtained the protein file and the GTF file.
I would like to merge the various files that were produced, but I am not sure what the best way to do this is.
My first concern is about the IDs in the predicted protein file, which have the same IDs. For example, all the FASTA files obtained with the predicted proteins have these IDs:
g1.t1 g2.t1 g3.t1 g4.t1 etc...
Is it necessary for me to modify the IDs in the individual files for each chromosome? That is, to specify in the protein IDs which files they come from, for example:
CH1_g1.t1 CH1_g2.t1 CH1_g3.t1 CH1_g4.t1 for the first chromosome, and CH2_g1.t1 CH2_g2.t1 CH2_g3.t1 CH2_g4.t1 for the second chromosome.
In this case, do I need to also modify the IDs in the GTF file?
Please, if you have a simpler solution to recommend, it would be greatly appreciated!
Which tools would you recommend for performing this operation?
Thank you very much for your help!
