I'm trying to convert a gff3 to gtf with gffread and i'm seeing unexpected filtering of most records in the gff3. it is for a viral genome. Only 10 out of 180 are going through. curiously, the first of these two records are converting, but the second is not:
EF999921.1 Genbank transcript 60089 60314 . + 1 ID=cds-ABV71552.1;Dbxref=NCBI_GP:ABV71552.1;Name=ABV71552.1;gbkey=transcript;product=UL22A;protein_id=ABV71552.1 EF999921.1 Genbank transcript 83771 83813 . - 1 ID=cds-ABV71567.1;Dbxref=NCBI_GP:ABV71567.1;Name=ABV71567.1;gbkey=transcript;product=UL37;protein_id=ABV71567.1
They seem to have the same types of information. The difference in these two examples is + and - but the full list that gets filtered in is a mix of + and -. codon start is also mixed.
Does the gff need to be sorted or prepped in any way? this file is ascii text with unix line terminators. very confused here.
my command is
path/to/cufflinks-2.2.1/gffread input.gff3 -T -o output.gtf