convert gff annotation file to gtf format
The purpose of the script is to convert NCBI virus gff format gene annotation file to gtf format, for running STAR, HTSeq-counts, etc
As a result, only 'exon' entries and related entries (parental of 'exon') are collected and reformated into a gtf file, other entries (e.g. 'intron') are discarded. The output gtf file includes the needed information such as 'gene_id', 'transcript_id', etc.
References:
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GFF3 format https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
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GFF/GTF conversion and differences http://blog.nextgenetics.net/?e=27