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How to download sequencing data from an NCBI Bioproject

This recipe downloads sequencing data from an NCBI project.

3 results • updated 4.3 years ago by Emily

This recipe downloads sequencing data from an NCBI project.

For more information see the

Bioinformatics Data Analysis oline course
Biostar Handbook for system setup and other information.

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#
# This recipe downloads sequencing data from an NCBI project.
#

#
# The script limits the number of runs and the number of reads that it unpacks from each run.
#

# Stop on any error. Print the commands as they execute.
set -uex

# NCBI BioProject ID.
PRJN=PRJNA257197

# How many sequencing runs to get for the project.
RUNS=5

# How many reads to download from each run.
READS=2000

# Obtain the run information.
esearch -db sra -query $PRJN | efetch -format runinfo > runinfo.csv

# Obtain the first few SRR numbers.
cat runinfo.csv | cut -f 1 -d , | grep SRR | head -$RUNS > runids.txt

# Create a directory for the sequencing data.
mkdir -p reads

# Download the FASTQ data for each SRR number.
cat runids.txt | parallel fastq-dump --split-files -X $READS --outdir reads {}

# Save quality control plots into a separate directory.
mkdir -p fastqc

# Run fastqc on each file. Generate the output into the fastqc directory.
fastqc -o fastqc reads/*.fastq

# Remove zip files created by fastqc
rm -f fastqc/*.zip

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Edit the content of each interface element.

[bioproject]
label = "BioProject Number"
display = "TEXTBOX"
value = "PRJNA257197"
help = "An NCBI project run number"
regex = "\\w{1,15}$"

[runs]
label = "Number of runs per project"
display = "INTEGER"
value = 5
range = [ 1, 100,]
help = "How many SRR runs to extract per project"

[reads]
label = "Number of reads per run"
display = "INTEGER"
value = 2000
range = [ 1, 10000,]
help = "How many reads to unpack per SRR run"

[settings]
name = "How to download sequencing data from an NCBI Bioproject"
help = "This recipe downloads sequencing data from an NCBI project.\n\nFor more information see the \n\n* [Bioinformatics Data Analysis][link] oline course\n* [Biostar Handbook][book] for system setup and other information.\n\n[link]: https://www.biostarhandbook.com/edu/course/4/\n[book]: https://www.biostarhandbook.com/"
template = "How_to_download_sequencing_data_from_an_NCBI_Bioproject_bio-data-analysis_79.sh"
image = "How_to_download_sequencing_data_from_an_NCBI_Bioproject_bio-data-analysis_79.png"
id = 79
recipe_uid = "ncbiproject"
uid = "ncbiproject"
url = "http://localhost8000"

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