The CCDS project tries to identify a core set of human and mouse protein coding regions in a stable manner.
There is always confusion about different notations of the start coordinates of genomic features between different genome browsers and file formats.
The phase (or sometimes called frame) gives information on how to translate individual parts of a gene, the coding exons. Phases 1 & 2 have a different definition in GFF and EnsEMBL format!
One of the most common question after your Next-Generation Sequencing (NGS) run is: “What is the coverage I achieved?” Unfortunately there a different definitions available for the term “coverage”.
To display data as bar graphs along the genome e.g. in the UCSC genome browser, you can create BigWig files. DeepTools is a powerful library that can also help with this.