I have two genomes and their gtf/gff file obtained from Ensembl. These genomes are related to each other but one of them is complete and other is at contig/scaffold level. I used Mauve Contig Mover (MCM) to rearrange the contigs in reference to the complete genome. Now I wish to merge the sequences inside the new file coming out of MCM and update alongside the gtf/gff files with new gene coordinates. Is their a tool with which we can achieve this?
Thanks in advance!!