Sam's Notebook

Data Wrangling - P.meandrina Genome GFF to GTF Using gffread

by Sam White ~1 min read

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):

20230519-pmea-gff_to_gtf.ipynb)

Jupyter Notebook (NBviewier):

20230519-pmea-gff_to_gtf.ipynb

RESULTS

Output folder: