how can I download Chromosome 1 of the human genome

Question

[alison.sw]

Hi there, I"m can't find the ftp address for a fasta file of the nucleotide sequences for GRCh38 Chromosome 1. NC_000001.11

I don't want to download the whole genome as I"m low on space. If anyone could point me in the right direction or a mirror site. that'd be great.

thanks

Answer 1

[MirianT_NCBI]

Hi,

You can use NCBI Datasets. You can use the following command (assuming you want to download the chromosome 1 from the Human Reference Sequence):

datasets download genome taxon human --reference --chromosomes 1 --filename human_chr1.zip

This will download a full data package that includes genomics fasta, protein, gff3, transcripts and cds sequences, plus metadata file.

If you want only the genomic fasta, here's the command (notice the --exclude flags):

datasets download genome taxon human --reference --chromosomes 1 --exclude-genomic-cds --exclude-protein --exclude-rna --exclude-gff3 --filename human_chr1_seq.zip

Let me know if this works for you or if you run into any issues. :)

[MirianT_NCBI]

You can also download it directly from the NCBI website. Click on "FASTA" on the left and "Send to" File on the right.

Here's the link to the FASTA record: https://www.ncbi.nlm.nih.gov/nuccore/NC_000001.11?report=fasta

[alison.sw]

great. I like those tools

Answer 2

[Pierre Lindenbaum]

https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/

[alison.sw]

I'm using a mac so I"m using curl is there something wrong with my syntax ? curl -L ftp://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fna.gz curl: (78) RETR response: 550

[Pierre Lindenbaum]

wrong url.

$ curl -s "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz" | gunzip -c | head
>chr1
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN