This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Where to find Download version of GRCh37 in NCBI

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?

gene genome
• 22,846 views • link
updated by Ram Ram • written by jesselee516 jesselee516

5 answers

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?

• 0 views • link
updated by Ram Ram • written by jesselee516 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.

• 0 views • link
written by jesselee516 jesselee516

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

• 0 views • link
written by KVC_bioinfo KVC_bioinfo

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

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

• 0 views • link
written by mt1022 mt1022

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

• 0 views • link
updated by Ram Ram • written by Dan D Dan D

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/

• 0 views • link
updated by Ram Ram • written by jesselee516 jesselee516

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).

• 1 views • link
updated by Ram Ram • written by niharraul • niharraul

You can download it here.

• 0 views • link
updated by Ram Ram • written by Emad • Emad

Log in to answer this question.

More posts like this