Question: GRCh37.p13 download at NCBI FTP?
0
gravatar for Marvin
26 days ago by
Marvin120
Australia
Marvin120 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 • 185 views
ADD COMMENTlink modified 24 days ago by Kevin Blighe30k • written 26 days ago by Marvin120
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 26 days ago • written 26 days ago by ATpoint8.0k
1

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

ADD REPLYlink written 26 days ago by Emily_Ensembl16k

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

ADD REPLYlink written 26 days ago by ATpoint8.0k

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

ADD REPLYlink written 26 days ago by Marvin120

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 26 days ago • written 26 days ago by cpad01129.3k
1
gravatar for Kevin Blighe
24 days ago by
Kevin Blighe30k
Republic of Ireland
Kevin Blighe30k 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 24 days ago by Kevin Blighe30k
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