There is a largely complete but some mistakes in it genomic reference with an accompanying annotation which has had some manual gene curation. I have some re-sequencing data for this genome and completed all the gaps and corrected errors of this genomic reference however a large number of the genes should not change as much of the sequence is the same. I am producing a new annotation now for it, using the transcripts from the old reference as evidence for maker2 software to generate the annotation because now the sequence does not contain 100 x N stretches throughout and corrected errors it needs re-annotating.
I would like to compare how many of the old genes are found in the new and what has changed for the publication. I'm thinking blast the two sets of transcripts and the 100% matches can say have not changed and thus confirmed using Maker2 software.
However those unique to the old reference and to the new I'm guessing I would have to be manually check? What stat's/comparisons can I use in the publication?
