How to convert to .SRA files to .FQ (FASTQ)
5
5
Entering edit mode
7.9 years ago

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 :)

fastq FASTQ sra RNA-Seq SRAA • 51k views
0
Entering edit mode

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

0
Entering edit mode

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

0
Entering edit mode

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

14
Entering edit mode
7.9 years ago
Ming Tang ★ 2.7k

They have fastq files ready for you.

0
Entering edit mode

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

11
Entering edit mode
7.9 years ago

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
0
Entering edit mode

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.

0
Entering edit mode

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:

You might want to try that.

0
Entering edit mode

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

Thanks :)

0
Entering edit mode

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

3
Entering edit mode
7.9 years ago
wynstep ▴ 80

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

0
Entering edit mode

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

Thanks again.

0
Entering edit mode

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

3
Entering edit mode
7.9 years ago

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

0
Entering edit mode

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 :/

0
Entering edit mode

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.

2
Entering edit mode
7.9 years ago
Manvendra Singh ★ 2.2k

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

0
Entering edit mode

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

0
Entering edit mode

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).

0
Entering edit mode

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

Traffic: 1896 users visited in the last hour
FAQ
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.