Working with GFF GFT GTF2 GFF3 reference annotation

• All annotation datatypes have a distinct format and content specification.
  • Data providers may release variations of any, and tools may produce variations.
  • GFF3 data may be labeled as GFF.
  • Content can overlap but is generally not understood by tools that are expecting just one of these specific formats.
• Best practices
  • The sequence identifiers must exactly match between reference annotation and reference genomes transcriptomes exomes.
  • Most tools expect GFT format unless the tool form specifically notes otherwise.
    • Get the GTF version from the data providers if it is available.
    • If only GFF3 is available, you can attempt to transform it with the tool gffread.
  • Was GTF data detected as GFF during Upload? It probably has headers. -Remove the headers (lines that start with a “#”) with the Select tool using the option “NOT Matching” with the regular expression: ^#
    • Redetect the datatype. It should be GTF once corrected.
  • UCSC annotation
    • Find annotation under their Downloads area. The path will be similar to: https://hgdownload.soe.ucsc.edu/goldenPath/<database>/bigZips/genes/
    • Copy the URL from UCSC and paste it into the Upload tool, allowing Galaxy to detect the datatype.

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{% snippet  faqs/galaxy/datasets_working_with_reference_annotation.md %}