Question: GRCh37.p13 download at NCBI FTP?
1
gravatar for Marvin
5 months ago by
Marvin130
Australia
Marvin130 wrote:

I'm lost at the NCBI FTP server. Which file contains all chromosomes of GRCh37.p13 in one fasta? The program that I want to use takes one fasta file as the reference sequence. At ftp://ftp.ncbi.nih.gov/genomes/Homo_sapiens/ARCHIVE/ I don't see GRCh37.p13 and I don't see a README file .. I'm a little bit stuck here.

reference grch37 ncbi • 511 views
ADD COMMENTlink modified 5 months ago by Kevin Blighe37k • written 5 months ago by Marvin130
1

You can get it from Ensembl ensemble =), downloading Homo_sapiens.GRCh37.dna.primary_assembly.fa.gz. Still GRCh19 is old. Any reason you do not go with GRCh38?

ADD REPLYlink modified 5 months ago • written 5 months ago by ATpoint13k
3

No, you can't get it from ensemble, but you can get it from Ensembl.

ADD REPLYlink written 5 months ago by Emily_Ensembl17k

Yes Ma'am. Apologies for my carelessness ;-)

ADD REPLYlink written 5 months ago by ATpoint13k

I know how to get it from ensembl, I was curious where NCBI hides the equivalent :-)

ADD REPLYlink written 5 months ago by Marvin130

Download GRCh37.p13 single fasta file from Gencode: ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19/GRCh37.p13.genome.fa.gz

or from here with index as well: http://bioinfo.hpc.cam.ac.uk/downloads/datasets/fasta/grch37/

ADD REPLYlink modified 5 months ago • written 5 months ago by cpad011211k
1
gravatar for Kevin Blighe
5 months ago by
Kevin Blighe37k
Republic of Ireland
Kevin Blighe37k wrote:

The NCBI record for GRCh37.p13 (GCF_000001405.25) can be found here: https://www.ncbi.nlm.nih.gov/search/?expt_dict=b&term=grch37.p13.

Click on Download and then select Genomic FASTA and RefSeq:

j

The tar file contains the complete NCBI version of the genome release in FASTA format.

Kevin

ADD COMMENTlink written 5 months ago by Kevin Blighe37k
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