As part of getting P.meandrina genome info added to our Lab Handbook Genomic Resources page, I will index the P.meandrina genome file (Pocillopora_meandrina_HIv1.assembly.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):
The notebook linked below was renamed to 20230705-pmea-gff_to_gtf.ipynb (commit 995027e)
20230519-pmea-gff_to_gtf.ipynb
Jupyter Notebook (NBviewier):
20230519-pmea-gff_to_gtf.ipynb
RESULTS
Output folder:
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GTF
20230519-pmea-gff_to_gtf/Pocillopora_meandrina_HIv1.genes.gtf (60MB)
MD5 checkum:
638abc4f5f115e7a32731ad24cc558fd