How to convert to .SRA files to .FQ (FASTQ)

Question

[Veli Kaan Aydin]

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

I also tried fastq-dump --split-files -A SRR121576.sra 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

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 formatted to do tuxedo software (I do not now any different way to rna-seq analyzing) Can you help me anyway to repair archive or to find new fastq file or convert sra to fastq.

Thank you :)

[wynstep]

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

[Devon Ryan]

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

[Veli Kaan Aydin]

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

Answer 1

[Ming Tommy Tang]

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

They have fastq files ready for you.

[Research Dog]

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

Answer 2

[Sebastian Boegel]

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:

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

[Veli Kaan Aydin]

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.

[Sebastian Boegel]

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.

[Veli Kaan Aydin]

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

Thanks :)

[aimanbarki]

How do I know that fastq-dump is using my downloaded sra object (following the 1st path but not the 2nd one)

Answer 3

[wynstep]

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! ;)

[Veli Kaan Aydin]

Omg :) Thank you so much :D How did you do that, I'm asking because I also need SRR121576, SRR121578 and SRR121579 :)

Thanks again.

[Devon Ryan]

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

Answer 4

[Jeff Stafford]

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

[Veli Kaan Aydin]

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 :/

[Jeff Stafford]

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.

Answer 5

[Manvendra Singh]

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.fastqand*_2.fastq` is reported in your same directory.

HTH

[caelyn5201314]

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 doesn't work ...

It throws the error: data bad version while constructing page map within virtual database module - failed

[Devon Ryan]

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).

[caelyn5201314]

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