Automatic emails explained

Answer: 

Top tip: If you are splitting a gene model, you need to account for all children, tidy up after yourself!



Error in Gene Annotation


Q1. How to mark genes with no stop and/or no start codon?


  • With a right click select the gene of interest and the option 'Edit information'

  • In the mRNA column select > Attributes > Add > Tag

Q2. How to mark genes with an insertion, deletion or substitution?


  • Create the edition with a right click directly on the genomic sequence, not in the gene manual annotation. Any of these types of editions, changes the manual annotation open reading frame (ORF), but not the gene assembly per se

  • With a right click select the gene of interest and the option 'Edit information'. Select 'Set Readthrough Stop Codon'

  • With a right click select the gene of interest and the option 'Edit information'. In the mRNA column select > Attributes > Add > Tag > type: Internal stop codon


VectorBase Apollo monthly summary


Q3. How to mark a gene manual annotation as finished or unfinished?


With a right click select the gene of interest and the option 'Edit information'. In booth the gene and mRNA columns select the appropriate status.


Q4. What is 'strand_not identical'?


There is a bug in Apollo whereby if you flip the strand of the prediction, e.g., if you started with an RNAseq read alignment, then it does not reverse the strand for the gene, only the underlying exons. Hence, a gff3 export of this locus will result in features mapped to both strands. VectorBase has reported to Apollo developers this bug. A temporary solution is to select the locus and make a duplicate, then delete the original. This does seem to resolve it. You can check by visualizing the gff3 file for the locus from the drop down menu using the 'Get GFF3' option.