As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I will index the M.capitata genome file (Montipora_capitata_HIv3.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):
https://github.com/RobertsLab/code/blob/master/notebooks/sam/20230127-mcap-gff_to_gtf.ipynb
Jupyter Notebook (NBviewier):
https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230127-mcap-gff_to_gtf.ipynb
RESULTS
Output folder:
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GTF
20230127-mcap-gff_to_gtf/Montipora_capitata_HIv3.genes.gtf (75MB)
MD5 checkum:
b83bef3d27f343c120e6965bf32827f5