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
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written
by
alison.sw •
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. :)
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
great. I like those tools
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
wrong url.
$ curl -s "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr1.fa.gz" | gunzip -c | head
>chr1
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NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
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