As part of getting these three coral species genome files (GitHub Issue) added to our Lab Handbook Genomic Resources page, I also need to get the coral endosymbiont sequence. After talking with Danielle Becker in Hollie Putnam’s Lab at Univ. of Rhode Island, she pointed me to the Cladocopium goreaui genome from Chen et. al, 2022 available here. Access to the genome requires agreeing to some licensing provisions (primarily the requirment to cite the publication whenever the genome is used), so I will not be providing any public links to the file. In order to index the Cladocopium goreaui genome file (Cladocopium_goreaui_genome_fa) using HISAT2 for downstream isoform analysis using StringTie and ballgown, I need a corresponding GTF 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/20230217-cgor-gff_to_gtf.ipynb
Jupyter Notebook (NBviewier):
https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230217-cgor-gff_to_gtf.ipynb
RESULTS
Output folder:
-
GTF
20230217-cgor-gff_to_gtf/Pver_genome_assembly_v1.0.gtf (197MB)
MD5 checkum:
97e69a850faf2e6d9b60df828ad02671
RESULTS
Output folder: