Docker and Singularity are very appealing software systems to run different operating systems or reproducible analysis steps by using “containers”. Here is a quick intro to get you started.
There are different ways to encode the quality scores in FASTQ files from Next-generation sequencing machines. This is important to find out before using the data and to convert between formats if necessary.
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!