Hi,

I have annotated a genome using Maker, the gff file of which I have used for running Stringtie to generate gene counts. Pipeline used to generate read counts:

Hisat2 - Samtools sort - Stringtie (yet to implement DEseq2)

I have used some pipelines to predict effectors using the assembled genome (fasta) file and not the annotated genome file (these effectors were not predicted by Maker, hence had to use different pipelines for their predictions), now I have a protein fasta file that contains the sequences of new genes (predicted) which are not present in the gff file generated by Maker. How could I incorporate the info of these additional genes in the gff file so that I can re-run Stringtie to get the gene counts of initially predicted genes + newly predicted effectors?

Tried using bwa mem to convert the protein fasta file to bed but no luck. I cannot think of any other alternative. Any suggestions/advise from the experts out there will be great???

Thanks