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How to download sequencing data via Entrez Direct

This recipe demonstrates the basic use of Entrez Direct from the command line

1 result • updated 23 months ago by Istvan Albert • needs authorization

This recipe demonstrates the basic use of Entrez Direct from the command line

The recipe has code that shows how to:

Download nucleotide and protein sequences associated with individual NCBI accession numbers.
Download sequence run information associated with NCBI bioproject ids.
Download nucleotide and protein sequences associated with an NCBI bioproject ids.

By default the script accesses BioProject PRJNA257197:

https://www.ncbi.nlm.nih.gov/bioproject/PRJNA257197/

For more information see the:

Biostar Handbook handbook
Applied Bioinformatics course

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# Turn on strict error checking.
set -uex

# Bioproject number.
PNUM=PRJNA272617

# Accession number.
ACC=AF086833

# Accession number AF086833 in Genbank format.
efetch -db nuccore -format gb -id $ACC > $ACC.gb

# Accession number AF086833 in Fasta format.
efetch -db nuccore -format fasta -id $ACC > $ACC.fa

# Select a subsequence from the genome.
efetch -db nuccore -format fasta -id $ACC -seq_start=1000 -seq_stop=1030

# Get the sequencing run information deposited for a project.
esearch  -db sra -query $PNUM | efetch -format runinfo > runinfo.csv

# What is inside of the runinfo file?
cat runinfo.csv | cut -d , -f 1,2,16 | head -3

# Get all genomic sequences deposited for a project.
esearch -db nucleotide -query $PNUM | efetch -format fasta > genomes.fa

# Get all protein sequences deposited for a project.
esearch -db protein -query $PNUM | efetch -format fasta > proteins.fa

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