As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the P.verrucosa genome file (Pver_genome_assembly_v1.0.fasta) using HISAT2, but need a GTF file to also identify exon/intro splice sites. Since a GTF file is not available, but a GFF file is, I needed to convert the GFF to GTF. Used gffread to do this on my computer. Process is documented in Jupyter Notebook linked below.
Jupyter Notebook (GitHub):
https://github.com/RobertsLab/code/blob/master/notebooks/sam/20230127-pver-gff_to_gtf.ipynb
Jupyter Notebook (NBviewier):
https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230127-pver-gff_to_gtf.ipynb
RESULTS
Output folder:
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GTF
20230127-pver-gff_to_gtf/Pver_genome_assembly_v1.0.gtf (48MB)
MD5 checkum:
c3cc8fb576bcf39dd17b6d229100aa56