I'm wanting to align some RNA-seq to mm10. I've read that you should align to the major release and not patch releases (https://www.biostars.org/p/342482/).
However I can't find the full genomic fasta and gtf files for mm10/GRCm38, instead just separate fasta files for each of the chromosomes and no gtf annotation file?(ftp://ftp.ncbi.nlm.nih.gov/genomes/archive/old_genbank/Eukaryotes/vertebrates_mammals/Mus_musculus/GRCm38/). Instead they only seem to exist for the patch 6 release (ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/635/GCA_000001635.8_GRCm38.p6).
I'm getting really confused where to get them from, do people tend to just align to the patch release? If not where can I find the full genomic fasta and gtf files for the major release? I've looked on ncbi and ensembl and keep looping back to the newest patch release version...
Any help appreciated, thank you!
Thanks, I hadn't come across the gencode website before!