Question: How do I download mm10 major release genomic fasta and gtf file?
0
gravatar for sg197
4 months ago by
sg19710
sg19710 wrote:

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!

ftp fasta genomic assembly gtf • 670 views
ADD COMMENTlink modified 4 months ago by 27atcggcta27150 • written 4 months ago by sg19710
3
gravatar for 27atcggcta27
4 months ago by
27atcggcta27150
27atcggcta27150 wrote:

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

ADD COMMENTlink written 4 months ago by 27atcggcta27150
1

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

ADD REPLYlink written 4 months ago by sg19710
3
gravatar for genomax
4 months ago by
genomax78k
United States
genomax78k wrote:

Get both directly from GENCODE.

ADD COMMENTlink written 4 months ago by genomax78k
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