Investigating the M. capitata and P. acuta GFF files in this script, I found that the existing annotations did not include any UTR information. Both species have a CDS track, and P. acuta has an exon track that parses the CDS track but does not include UTR information. Two other coral methylation papers for different species (Aiptasia and S. pistillata) have genome annotations with CDS and exons (includes UTR) (see this issue).
Ideally, we would like to generate an exon track that has UTR information so we can easily compare our findings with previously published papers. @kubu4, do you know what sort of genome annotation tools we can use to do this?
Investigating the M. capitata and P. acuta GFF files in this script, I found that the existing annotations did not include any UTR information. Both species have a CDS track, and P. acuta has an exon track that parses the CDS track but does not include UTR information. Two other coral methylation papers for different species (Aiptasia and S. pistillata) have genome annotations with CDS and exons (includes UTR) (see this issue).
Ideally, we would like to generate an exon track that has UTR information so we can easily compare our findings with previously published papers. @kubu4, do you know what sort of genome annotation tools we can use to do this?