Question: How to convert to .SRA files to .FQ (FASTQ)
4
gravatar for Veli Kaan Aydin
3.3 years ago by
Turkey
Veli Kaan Aydin40 wrote:

Hello Everyone,

I'm trying to convert SRR121576, SRR121577, SRR121578, SRR121579 files to fastq format. I am using ubuntu software and after a long way searching web I found some commands and I tried "fastq-dump -A SRR121576 -D SRR121576.sra" Command And I got "

 

2014-08-13T08:53:37 fastq-dump.2.1.7 err: option -D is deprecated, see --help
2014-08-13T08:53:38 fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR121576.sra"  this error also I tried "fastq-dump --split-files -A SRR121576.sra" command and I got "014-08-13T08:54:49 fastq-dump.2.1.7 err: data bad version while constructing page map within virtual database module - failed SRR121576.sra
Written 0 spots total"  these commad

But after I failed, I tried only searching web to find directly .fastq after seaching I found ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/SRR121577/ this ftp but when I tried to gunzip or archivemanager or winrar with wine all of them failed because of this files corrupted. I tried download again but also it did not work. To sum up, I need these files as .fq formatte to do tuxedo software (I do not now any different way to rna-seq analyzing) Can you help me anyway to repeir archive or to find new fastq file or convert sra to fastq.

Thank you :)

 

 

 

 

 

 

rna-seq sraa fastq sra • 23k views
ADD COMMENTlink modified 3.2 years ago by Manvendra Singh1.9k • written 3.3 years ago by Veli Kaan Aydin40

I'm trying to download the archive and unpacking it. I'll let you know

ADD REPLYlink written 3.3 years ago by wynstep70

FYI, I've gotten a few "corrupted files" from ENA that turned out to have been submitted that way.

ADD REPLYlink written 3.3 years ago by Devon Ryan73k

Thank you for information, I'm trying wynstep's and Boegel's answer I hope I'll find solution. 

ADD REPLYlink written 3.3 years ago by Veli Kaan Aydin40
9
gravatar for Sebastian Boegel
3.3 years ago by
Germany
Sebastian Boegel420 wrote:

I suggest downloading the latest sratoolkit from http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software (which is currently, 2.3.5-2).

Now, either:

i) you download the sra and do path/to/sratoolkit.2.3.5-2-centos_linux64/bin/fastq-dump SRR121576.sra

ii) or you can skip the download step and do path/to/sratoolkit.2.3.5-2-centos_linux64/bin/fastq-dump SRR121576, which downloads and convert.

Useful options:

--gzip will gzip the fastq

--split-3 is for paired end reads

ADD COMMENTlink written 3.3 years ago by Sebastian Boegel420

Hello Sebastian,

First thank you for answer, I already download and install latest version (Also I configured it as they so ) But still I get errors while I'm trying codes I still gets those errors. 

ADD REPLYlink written 3.3 years ago by Veli Kaan Aydin40

Mmh weird. It worked for me. You downloaded your file from EBI, right? Maybe the sra file stored there is somehow corrupted as Devon wrote above. I downloaded via the link provided at the NCBI SRA page for the sampel which is:

wget ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR121/SRR121576/SRR121576.sra

YOu might want to try that.

 

ADD REPLYlink written 3.3 years ago by Sebastian Boegel420

Yes, I tried that source but I'm going to try all of it again.

Thanks :)

ADD REPLYlink written 3.3 years ago by Veli Kaan Aydin40
9
gravatar for tangming2005
3.3 years ago by
tangming20052.2k
Houston/MD Anderson Cancer Center
tangming20052.2k wrote:

got to EBI http://www.ebi.ac.uk/ena/data/view/SRR121576

They have fastq files ready for you.

ADD COMMENTlink written 3.3 years ago by tangming20052.2k

This way is better than fastq-dump. EBI has fastq files to squarely download and use.

ADD REPLYlink written 15 months ago by 7667069030
3
gravatar for wynstep
3.3 years ago by
wynstep70
wynstep70 wrote:

I successfully downloaded and extracted your file. You can download it from my own server:
160.80.35.140/temp_file

I will delete the file tomorrow morning, so be quick! ;)

ADD COMMENTlink written 3.3 years ago by wynstep70

Omg :) Thank you so much :D How did you do that, I'm asking because I also need SRR121576 (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/SRR121576/)  

SRR121578 (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/SRR121578/) and

SRR121579 (ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR121/SRR121579/)  :)

Thanks again.

ADD REPLYlink written 3.3 years ago by Veli Kaan Aydin40

FYI, I've moved this to an answer, hope you don't mind.

ADD REPLYlink written 3.3 years ago by Devon Ryan73k
3
gravatar for Jeff Stafford
3.3 years ago by
Canada
Jeff Stafford50 wrote:

Download sra-toolkit from NCBI SRA. Download the runs you want from NCBI SRA if you don't have them already.

Use the syntax: "fastq-dump <yourFileHere.sra>". Add --split-files if you're dealing with paired-end reads.

I'm looking at the documentation and the -A & -D aren't listed as valid options... http://www.ncbi.nlm.nih.gov/Traces/sra/?view=toolkit_doc&f=fastq-dump.

ADD COMMENTlink written 3.3 years ago by Jeff Stafford50

Thank you for answering my question, and I know it is not listed but since I'm trying the commands I already try lots of them :/

ADD REPLYlink written 3.3 years ago by Veli Kaan Aydin40

Totally understand the feeling... once I spent two or three days trying to get the fastx-toolkit to work only to find that it needs the secret "-Q33" option before it can read new Illumina files. Of course this option/issue wasn't in any of the documentation and I spent days bashing my head into the keyboard until I stumbled on a well-hidden forum post that mentioned it.

ADD REPLYlink written 3.3 years ago by Jeff Stafford50
1
gravatar for Manvendra Singh
3.2 years ago by
Manvendra Singh1.9k
Berlin, Germany
Manvendra Singh1.9k wrote:

I always use the command and it has always worked

fastq-dump --split-3 *.sra

for any kind of .sra file, if its single end then one output as *.fastq and if its paired end then  *_1.fastq and *_2.fastq is repoted in your same directory.

 

HTH

ADD COMMENTlink written 3.2 years ago by Manvendra Singh1.9k

Hi sorry to bother you...I use the command "fastq-dump --split-3 *.sra" 

the problem is for the single end it works but for the paired end it doesnt work ...

it throw the err:data bad version while constructing page map within virtual database module - failed 

ADD REPLYlink written 3.0 years ago by caelyn520131410

See if there's a newer version of fastq-dump. They update it on occasion and there's little in the way of backwards compatibility (one of the many reasons people try to avoid SRA format).

ADD REPLYlink written 3.0 years ago by Devon Ryan73k

thank you very much !!! It worked !!!

ADD REPLYlink written 3.0 years ago by caelyn520131410
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