Probably a basic question but it's difficult to find information on the subject...
When viewing a GTF and BED file in IGV, there seems to be differences in colour (BED track can't be recoloured, just shows as black, GTF can be recoloured). Does anyone know the reason for this? I thought that the GTF and BED formats contained predominantly the same information just in different formats.
A GTF file is more akin to a large group of BED files grouped according to some feature or features of relevance, often with multiple levels of hierarchical metadata. In the classical case of genes, GTF specifies a standard way of relating exons to transcripts and genes. There's no standard way of doing that with BED files. BED files are useful for cases where the file itself contains only a single type of information (e.g. ChIP-seq peaks), where you could instead combine multiple of these files in a GFF (e.g., annotating peaks from different histones pulled down with multiple antibodies each). You can do some of this by using the `name` field in the BED format, but there's still no good way to represent hierarchical.
BED was originally designed to contain color specification for each row in column 9. In addition it can contain a number of track definitions in the header that can further specify the colors. Using these have fallen out of favor (thankfully so I might add) but IGV seems to stick with the more strict definition of reading the color from the rows themselves.
