There is a genome in unoriented and unorder scaffolds. I am interested in a specific area of the genome. Therefore I managed to align the scaffolds to a closely related species and I got an idea about the orientation of the scaffolds.
Do you know any way to change the orientation inside the genbank file of those scaffolds? In order to upload it later to a genome viewer such as Artemis?
Any help please. Thanks a lot.
eg. is there any way to merge the scaffolds and add one CDS next to the other, in the correct way? In biopython?