Question: NCBI vs ENSEMBL FASTA
0
gravatar for uki_al
2.1 years ago by
uki_al50
uki_al50 wrote:

Hi I have a question about the differences between the FASTA files that can be downloaded from the ensembl ftp (ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/dna/Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz) and the ncbi ftp (ftp://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/annotation/GRCh37_latest/refseq_identifiers/GRCh37_latest_genomic.fna.gz).

As far as I could get tell, both are GRCH37 versions, so I was curious are the references identical or not? If they are, could I use the FASTA file downloaded from the ensembl ftp together with the gene-annotation file downloaded from ncbi ftp?

I know UCSC differs by chromosome naming, and I know there are tools that can convert from one to another, that's why I opt to download UCSC FASTA and GTF and use them together. I was also using up until now the ensembl FASTA and GTF together. But I was just curious, if I want to use ncbi GTF, do I need to download the FASTA from the ncbi ftp, or will the ensembl one do the job? From what I understood, they should be identical, I just couldn't confirm this...

ADD COMMENTlink modified 22 months ago by Biostar ♦♦ 20 • written 2.1 years ago by uki_al50
1
gravatar for Jean-Karim Heriche
2.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche19k wrote:

The assembly may be the same although they could differ due to the differential application of patches. Regardless, the annotations would definitely be different between the different resources as they each annotate the genome in their own way. Switching between or mixing references during a project is asking for trouble.

ADD COMMENTlink written 2.1 years ago by Jean-Karim Heriche19k
2

For reference: chromosome coordinates remain unchanged by patches.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by genomax68k

Thanks, I wasn't sure about that.

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche19k
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