Where to find Download version of GRCh37 in NCBI

Question

[jesselee516]

Hi,everybody,

I find that the lastest version of gene in NCBI is GRCh38,I could find GRCh37 for on-line browser version. But I can not find the download version.In the download page, The only version is GRCh38. Anyone know where to download GRCh37 download files in NCBI?

Answer 1

[Pierre Lindenbaum]

under ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3

[jesselee516]

Hi Pierre, Thanks for reply.The link is right. But the version is not the latest GRCh37 version. The latest version should be GRCh37.p13 Primary Assembly. Got any has idea?

[Siva]

Is this the one you are looking for?

ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/

[jesselee516]

Hi Pierre, Thanks for your help. The file in GFF fold is just what I need. Thanks again. You did help me a lot.

[KVC_bioinfo]

Is there any way I can download all the chromosomes in one file instead of separate file?

Answer 2

[mt1022]

ENSEMBL has a dedicated site for GRCh37 with annotations files updated about every 6 months:

http://grch37.ensembl.org/index.html

Answer 3

[Dan D]

Dunno about NCBI, but you can get the latest GRCh37 reference here.

[jesselee516]

Thanks for your reply. These files are FASTA format sequence. That is useful for. My additional question is if I could get info like 'gene location,exon/intro location' etc. What I need Info looks like gene2accession.gz that kind of info? What I mean is gene info looks like file in ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/

[summerela]

It sounds like you want the GTF files: ftp://ftp.ensembl.org/pub/release-75/gtf/homo_sapiens/README

Answer 4

[niharraul]

I came across this post while searching for a download link for retrieving GRCH 37 refseq assembly, since I see there are 2 links being posted by Pierre and Dan(ESEMBL sequences/transcript).

1. Now, for my requirement (GRCh37 + refseq) I should be using the link provided by Pierre.
2. Moreover, when I use the link provided by Pierre, I see there are lot of files for a given chromosome and is it GRCH37:

hs_ref_GRCh37.p13_chr1.fa.gz
hs_ref_GRCh37.p13_chr1.asn.gz
...
...
hs_al_CHM1_1.1_chr1.asn.gz
hs_al_CHM1_1.1_chr1.fa.gz
Hs_alt_HuRef_chr1.asn.gz
...
...

It would be great, if someone could guide me whether I use the correct file hs_ref_GRCh37.p13_chr1.fa.gz to retrieve the entire genomic sequence for chromosome 1 (refSeq).

[5heikki]

Ftp dirs at the NCBI generally have README files. Did you check it?

ftp://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/ARCHIVE/BUILD.37.3/README

Answer 5

[Emad]

You can download it here.