Working with GFF GFT GTF2 GFF3 reference annotation

Authors:

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.

Resource PURL: https://gxy.io/GTN:F00052