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Old 05-23-2011, 03:15 AM   #1
TuA
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Question How convert multiple .sra files into .fastq in one go?

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!
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Old 05-23-2011, 05:03 AM   #2
Dethecor
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Default bash scripts 4tw

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

Code:
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
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Old 05-23-2011, 05:07 AM   #3
TuA
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This is great! Thanks a lot! I'll check what my machine can do ;-)
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Old 05-23-2011, 12:17 PM   #4
tldgID
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Question 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!
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Old 05-27-2011, 09:31 AM   #5
TuA
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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?
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Old 05-27-2011, 09:32 AM   #6
TuA
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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?
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