Download NCBI data using sratoolkit in anaconda

Question

[sooni]

Hello

I would like to download data from the PRJNA834801 project for analysis practice. I succeeded in installing sratoolkit in anaconda. How do I download all the data (725 data sets in the BioProject) of the project I want to download at once?

Please help me.

Thank you. :)

[andres.firrincieli]

How do I download all the data (725 data sets in the BioProject) of the project I want to download at once?

This is a very basic task... after installing sratoolkit what did you try?

[GenoMax]

You can also use the program mentioned here: Access to fastq files on SRA Run browser

Note: This is close to 2TB of data so make sure you have enough bandwidth and storage available.

Answer 1

[Istvan Albert]

you could use my bio package to get all the SRR numbers

pip install bio 

then

bio search PRJNA834801 --csv > runinfo.csv

and then loop over all the SRR numbers to fetch the data

cat runinfo.csv | csvcut -c 1 | parallel fastq-dump -X 1000 --split-files -o reads {}