Using Container Software
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.
Category: bioinformatics
RNA-Seq data quality scores
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
The CCDS project tries to identify a core set of human and mouse protein coding regions in a stable manner.
Genomic Start Coordinates
There is always confusion about different notations of the start coordinates of genomic features between different genome browsers and file formats.
Coding Phases / Frames
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!