download all samples from a study in BioProject

Question

[ifudontmind_plzz]

How to download all samples (fastq files) in a particular study (e.g., PRJNA223640) from bioproject.

[ifudontmind_plzz]

i did manage to downlaod th run data one after each other.

Answer 1

[piet]

If you want to download from NCBI, then the key is to get the so-called 'runinfo' file. The 'runinfo' file is a simple CSV table which lists sequencing runs in the 'sra' database and their download links. After you have obtained the 'runinfo' file, you can write a short script to download the run data one after each other.

You can download the 'runinfo' file with wget:

wget 'http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?save=efetch&rettype=runinfo&db=sra&term=PRJNA223640' -O - | tee SraRunInfo.csv

[ifudontmind_plzz]

great. could you show a sample script to download the run data?

[piet]

This project comprises about 150 sequencing runs. Each run has a size of more than 1 Gb. You should have a good concept of how to organize and further process the data before actually starting the download.

[ifudontmind_plzz]

yes. Is there any way to process this data.

[110300553]

Echoing ifudontmind_plzz would it be possible to get an example of the code to use the csv file for the download?

[rodd]

Is this command provided by piet still supposed to work? It returned an empty file for me.

[UPDATE] I realised my bioproject does not have SRA files, but "biosamples" - that's why it's not working..