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Type: Improvement
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Status: Closed
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Priority: Major
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Resolution: Fixed
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Affects Version/s: 1.32
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Fix Version/s: 33
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Component/s: Basic-Nucl
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Labels:
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Story Points:3
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Sprint:DEV-33-2
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Affect Type:Userdefined
Currently the 9th attribute column of a GTF is parsed into qualifiers of the corresponding annotations, however, all qualifiers are called "attr". See the attached screenshot.
For example, for the following line:
chr20 ensembl_havana gene 87250 97094 . + . gene_id "ENSG00000178591"; gene_version "6"; gene_name "DEFB125"; gene_source "ensembl_havana"; gene_biotype "protein_coding";
a "gene" annotation should be created with the following qualifiers:
- gene_id (with value "ENSG00000178591" without quote marks).
- gene_version
- gene_source
- etc.
As sample data use, for example, files "Homo_sapiens.GRCh38.dna.chromosome.20.fa.gz" (a sequence) and "chr20_ref.gtf" (the corresponding GTF file), located in the ".../test/UGENE-6398" folder on the file server.
- relates to
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UGENE-6406 GTF parsing errors for chr20.gtf
- Closed