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Download NCBI data using sratoolkit in anaconda

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. :)

ncbi sratoolkit anaconda
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updated by Ram Ram • written by sooni • sooni

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?

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written by andres.firrincieli andres.firrincieli

1 answer

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 {}
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written by Istvan Albert Istvan Albert

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