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genePred
The genePred table formats can be used to specify the gene track annotations for an imported genome.
Several variations of the genePred table format are described in the FAQ titled “genePred table format” on the UCSC Genome Browser web site: http://genome.ucsc.edu/FAQ/FAQformat#format9. Downloading gene information from any of these tables creates a tab-delimited text file where the columns in the file match the columns in the table. Downloaded files may be zipped with a .txt.gz extension. Such a zipped file can be used to specify the gene track annotations for an imported genome. IGV looks for specific string in the filename (case insensitive) to identify the file format:
| File Name Contains | Description |
|---|---|
| ucscGene | Columns in the file match the columns in the table, as described in the “Gene Predictions” section of the genePred table format FAQ. |
| genePredExt refGene ensGene |
These files have the same format. Columns in the file match the columns in the table, as described in the “Gene Predictions (Extended)” section of the genePred table format FAQ. Note: The first column of this file holds an integer, which is not documented in the FAQ and is ignored by IGV. |
| refFlat | Columns in the file match the columns in the table, as described in the “Gene Predictions and RefSeq Genes with Gene Names” section of the genePred table format UCSC FAQ. |