How convert multiple .sra files into .fastq in one go?

[TuA]

Hi all,

I have hundreds of .sra files of a genome re-sequencing project which I downloaded from the NCBI sequence read archive. Does anyone know a quick way of converting them into fastq files? With the SRA toolkit it seems to work with only one file at the time:

../bin64/fastq-dump -A <SRR_accession> -D <Path_to_SRR_Directory> -O <Output_Path>

Many thanks for your suggestions!

[Dethecor]

bash scripts 4tw

Assuming you're running bash (otherwise the syntax might be slightly different):

for fn in *.sra
do
../bin64/fastq-dump $fn
done

This will take all *.sra files in the current directory and convert them into corresponding fasta-files.

If you are on a powerful machine you might want to add an & to the end of the call to fastq-dump in order to start all of this simultaneously (risking angry glares from other users and/or the admin once the machine crashes ).

Cheers,
Paul

[TuA]

This is great! Thanks a lot! I'll check what my machine can do ;-)

[tldgID]

many samples?

Hi TuA,

Can I ask if the data that you downloaded, is from multiple samples or it's just one sample? The reason for this question is that I am looking for NGS datasets with multiple samples, ideally from 2 different phenotypes. And “hundreds of .sra files of a genome re-sequencing project” gave me hope for finding many samples

Thank you!

[TuA]

Hi tldgID

Sorry for not responding earlier. I'm afraid I don't think the data will be of use for you. I actually downloaded data from different projects on mammals but with only 1-2 samples per species and no phenotype info...

I guess you checked the experiments/studies on SRA?

[TuA]

Hi tldgID

Sorry for not responding earlier. I'm afraid I don't think the data will be of use for you. I actually downloaded data from different projects on mammals but with only 1-2 samples per species and no phenotype info...

I guess you checked the experiments/studies on SRA?