How do I download mm10 major release genomic fasta and gtf file?
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2.2 years ago
sg197 ▴ 30

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!

assembly gtf fasta ftp genomic • 4.9k views
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2.2 years ago
27atcggcta27 ▴ 170

As genomax pointed out you can get both from the gencode website. Just google gencode mouse and it should be the first hit (or just follow the link posted by genomax)

for the GTF file, You will probably want the Comprehensive gene annotation for CHR region. just copy the link and use wget -c to download, then gunzip. The link Im talking about is ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/gencode.vM22.annotation.gtf.gz

for the fasta file, you will probably want the Genome sequence (GRCm38.p6). Again, just copy the link from gencode and use wget -c and then gunzip. here is the link for clarity: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M22/GRCm38.p6.genome.fa.gz

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Thanks, I hadn't come across the gencode website before!

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2.2 years ago
GenoMax 109k

Get both directly from GENCODE.

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