Details
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Type:
Improvement
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Status: Open
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Priority:
Major
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Resolution: Unresolved
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Affects Version/s: None
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Fix Version/s: None
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Component/s: file format issue, sequencefeatures
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Labels:None
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Epic Link:
Description
Some programs have different levels of support for GFF, and custom interpretations
IGV seems to allow pragmas for changing how the fields are interpreted (or shown) - e.g. https://software.broadinstitute.org/software/igv/GFF ##displayName can be used to specify the display name field. The Column 9 'Color' attribute can be used to specify the colour for a feature.
UCSC Genome browser only supports GFF2 - and treats column 9 as a 'group' tag (putting all features with the same col. 9 value in the same group) - so an option to restrict or simplify the output of column 9 could be useful here. see https://genome.ucsc.edu/FAQ/FAQformat.html#format3
IGV seems to allow pragmas for changing how the fields are interpreted (or shown) - e.g. https://software.broadinstitute.org/software/igv/GFF ##displayName can be used to specify the display name field. The Column 9 'Color' attribute can be used to specify the colour for a feature.
UCSC Genome browser only supports GFF2 - and treats column 9 as a 'group' tag (putting all features with the same col. 9 value in the same group) - so an option to restrict or simplify the output of column 9 could be useful here. see https://genome.ucsc.edu/FAQ/FAQformat.html#format3