A few more tips here

I have recently needed the same functionality and came up with a one-liner that gets all the data from a BioProject. It requires Entrez Direct (Ncbi Releases Entrez Direct, The Entrez Utilities On The Unix Command Line ) and SRA toolkit (although the former package could easily be replaced with simple wget commands)

This below will only download the first 5 datasets and only 10 spots from each as a demo, removing those limitations will get all 216 files and hundreds of millions of spots:

esearch -db sra -query PRJNA40075  | efetch --format runinfo | cut -d ',' -f 1 | grep SRR | head -5 | xargs fastq-dump -X 10 --split-files

More adventurous people might want to pipe the output into parallels instead of xargs thus fully saturating their bandwith.

How to change the default fold of the downloading for prefetch? usually, the home directory is not big enougth for large number of SRA files?

/home/[USER]/ncbi/public/sra/

Please be sure you sra-tools is always the lastest version or else some strange error maybe come out!

Eventually, I find we can re-set the cache directory by the following step:

1. come to bin directory, such as: /home/sratoolkit.2.5.5-centos_linux64/bin
2. ./vdb-config -i
3. change the fold of Workspace Name to a big harddisk.

Re-run fastq-dump, the cache files will come to new setted directory.

Remember: There will be large files in: /home/shg047/oasis/ncbi/public/sra/sra, Be sure to remove them periodically.

One option is to download the fastq file and directly follow the pipeline. On some exome sequencing data fastq dump doesnt work as efficiently or gives errors as the deposited data is in bam format and requires genome file. So from the below website we can directly download the fastq files for all sequencing experiments in GEO.

ftp://ftp.sra.ebi.ac.uk/vol1/fastq/

Hi, I modified a bit the code so I can download several experiments from a download_list.txt (sample+'\t'+SRXcode). Unfortunately it only works for the first item in the list. It's something in the loop because they work fine separately. Any ideas? Thanks.

# -*- coding: utf-8 -*-

while read p1 p2; do
#Get SRR
srr="$(esearch -db sra -query $p2 | efetch -format runinfo | cut -d ',' -f 1 | grep SRR)"
prefetch $srr && vdb-validate $srr && fastq-dump --split-files $srr
done <download_list.txt

Addition:(Further Downstream RNA-Seq Analysis using GALAXY)

In case anybody wants to get files from SRA directly into GALAXY for further analysis, please check out this other video too, Video: RNA-Seq Alignment and Visualization using Galaxy and IGB. It explains how to get data from SRA directly into GALAXY using Tools in GALAXY itself.

I found this one useful so thought to share.

When I performed this

fastq-dump --outdir ~/Documents/USER/Re-analysisGPS2/fastq/ --split-files /home/USER/ncbi/public/sra/SRR1291261.sra

I did not receive 2 fastq file but only one file . Example: SRR1291261_1.fastq

Kindly suggest me what could be the reason? Is it because its not paired end?

Note that it might be necessary to convert the *.sra to *.fastq using some special parametres supplied to fastq-dump to make it suitable for Trinity assembly (to take care of the read names), i.e. for paired reads:

SRA_TOOLKIT/fastq-dump --defline-seq '@$sn[_$rn]/$ri' --split-files file.sra

see https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trinity-FAQ#ques_sra_fq_conversion

Just an update using the docker from sra-tools:

docker run -v $PWD:$PWD quay.io/biocontainers/sra-tools:3.1.1--h4304569_2 prefetch SRR28520745 --output-directory $PWD/
docker run -v $PWD:$PWD quay.io/biocontainers/sra-tools:3.1.1--h4304569_2 fastq-dump --outdir $PWD/SRR28520745/ --split-files $PWD/SRR28520745/SRR28520745.sra

How to use NCBI SRA toolkit effectively: Read this post https://reneshbedre.github.io/blog/fqutil.html