Downstream analysis to evaluate and annnotate gene predictions

See the scripts used for downstream evaluation here .

1. Run Mikado Compare to compare prediction with known annotation

2. Run Salmon to quantify predictions

3. Run Ribotricer to verify translation signal for predicted protein coding genes

4. Run BUSCO to see how well the conserved genes are represented in your final predictions

5. Run OrthoFinder to find and annotate orthologs present in your predictions

6. Run phylostratR to find orphan genes in your predictions [For theory and details, see: https://doi.org/10.1093/bioinformatics/btz171]

7. You can also add functional annotation to your genes using homology and InterProScan (We didn’t have this step in our paper).