Sam’s Notebook

University of Washington - Fishery Sciences - Roberts Lab

Posts

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

  • ~1 min read

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.verrucosa genome file (Pver_genome_assembly_v1.0.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.

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Data Wrangling - M.capitata Genome GFF to GTF Using gffread

  • ~1 min read

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.

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

  • ~1 min read

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.

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