Gencode sequence (GRCm38.p6) vs Gencode sequence, primary assembly (GRCm38)

Question

[pvd2107]

Hi, would someone be able to quickly explain the difference between these two fasta files to me? I'm not sure I understand as they are described on the Gencode site:

https://www.gencodegenes.org/mouse/

Thank you, Paul

Answer 1

[Bastien Hervé]

GRCm38, primary assembly is the major release 38 of mouse genome. You will find reference chromosomes (1-19, X, Y) + scaffolds parts

GRCm38.p6 is the 6th minor release of the major release 38 of the mouse genome. Those minor releases are minor modifications from the mouse genome in the associate major release. When GRC will decide to create a new major release, minor modifications from GRCm38 will be apply to the new GRCm39. You will find reference chromosomes (1-19, X, Y) + scaffolds parts + assembly patches + haplotypes

See also :

• Which human reference genome should I use?
• Filtering out chromosomes from reference genome
• https://www.ncbi.nlm.nih.gov/grc/help/definitions/

[pvd2107]

Great thanks a lot Bastien. Very helpful! From the links you sent me the primary assembly is the appropriate input for alignment, which is the clarification I needed.