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

TuA · 05-23-2011, 03:15 AM

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 · 05-23-2011, 05:03 AM

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

TuA · 05-23-2011, 05:07 AM

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

tldgID · 05-23-2011, 12:17 PM

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 · 05-27-2011, 09:31 AM

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 · 05-27-2011, 09:32 AM

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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05-23-2011, 03:15 AM	#1
TuA Junior Member Location: CH Join Date: May 2011 Posts: 9	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!

05-23-2011, 05:03 AM	#2
Dethecor Member Location: Germany Join Date: May 2010 Posts: 24	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 __________________ "You are only young once, but you can stay immature indefinitely."

05-23-2011, 12:17 PM	#4
tldgID Member Location: USA Join Date: May 2011 Posts: 18	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!

05-23-2011, 05:07 AM	#3
TuA Junior Member Location: CH Join Date: May 2011 Posts: 9	This is great! Thanks a lot! I'll check what my machine can do ;-)

05-27-2011, 09:31 AM	#5
TuA Junior Member Location: CH Join Date: May 2011 Posts: 9	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?

05-27-2011, 09:32 AM	#6
TuA Junior Member Location: CH Join Date: May 2011 Posts: 9	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?