Hello,
I am trying to extract_splice_sites using the python script provided by HISAT2 to use in the downstream alignment in HISAT2. However the reference genome that I am using, the most recent version, has a gff3 file with the gene annotation. I am unable to extract spliced sites with this gff file. Does anyone know a way to extract splice sites from a gff3 that can be used with the Hisat2 program? I have a gtf file but it was built on an older version of the genome assembly so I would prefer to use the newest (gff3).
Thank you for any help you can provide
I am trying to extract_splice_sites using the python script provided by HISAT2 to use in the downstream alignment in HISAT2. However the reference genome that I am using, the most recent version, has a gff3 file with the gene annotation. I am unable to extract spliced sites with this gff file. Does anyone know a way to extract splice sites from a gff3 that can be used with the Hisat2 program? I have a gtf file but it was built on an older version of the genome assembly so I would prefer to use the newest (gff3).
Thank you for any help you can provide
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