Data Wrangling - P.acuta Genome GFF to GTF Conversion Using gffread

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.acuta genome file 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/20230126-pacu-gff_to_gtf.ipynb

Jupyter Notebook (NBviewier):

https://nbviewer.org/github/RobertsLab/code/blob/master/notebooks/sam/20230126-pacu-gff_to_gtf.ipynb

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RESULTS

Output folder:

• 20230126-pacu-gff_to_gtf

  GTF

  • 20230126-pacu-gff_to_gtf/Pocillopora_acuta_HIv2.gtf (61MB)

  • MD5 checkum: 14f8c9bdd2ce4f3d713baf211469c13f