Converting .sra files to fastq

Question: Converting .sra files to fastq

4.0 years ago by

Linda • 150

India

Linda • 150 wrote:

I am trying to convert .sra files to fastq using fastq-dump on a CentOS machine. I already have the sra files downloaded so I do not want to redownload them. The command sratoolkit.2.3.5-2-centos_linux64/bin/fastq-dump SRR554454.sra seems to do nothing. There is no error, no output, and it does not seem to be using up any cpu or network either. What am I doing wrong?

fastq sra • 6.4k views

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modified 4.0 years ago by piet • 1.4k • written 4.0 years ago by Linda • 150

You are using the correct command. This link says "fastq-dump would still attempt to contact NCBI to obtain the references needed to convert the data to fastq". So is it possible that there is a network connection problem? I would suggest using a small dataset first, since the process takes a while. And also try to do "fastq-dump SRR554454" directly, which download the data from SRA and then output the data in fastq format.

ADD REPLY • link modified 4.0 years ago • written 4.0 years ago by Zhaorong • 1.2k

it's important to use the --split-files if it is paired end, otherwise you will get a very messy fastq file

ADD REPLY • link written 4.0 years ago by eddie.im • 130

you sure the sra file is in the same directory as you invoke fastq-dump?

ADD REPLY • link written 4.0 years ago by Ming Tang • 2.3k

4.0 years ago by

Varun Gupta • 1000

United States

Varun Gupta • 1000 wrote:

HI,

I just downloaded the file and used this and it worked

/apps1/sratoolkit/2.3.3-2/bin/fastq-dump --split-files SRR554454.sra

2 separate files are produced (paired end) SRR554454_1.fastq SRR554454_2.fastq

ADD COMMENT • link written 4.0 years ago by Varun Gupta • 1000

This does nothing in my case, as before, no activity at all, or error. Does this try to connect to ncbi even if the sra file is downloaded?

ADD REPLY • link written 4.0 years ago by Linda • 150

Apparently it does need to connect to ncbi. Once I moved to a machine outside the firewall, it worked fine.

ADD REPLY • link written 4.0 years ago by Linda • 150

4.0 years ago by

piet • 1.4k

planet earth

piet • 1.4k wrote:

according to this recipe I used option '-A' to convert a file which I had already downloaded locally. For debugging it may also help to set option '-v' once or several times.

fastq-dump -v -A ./SRR554454.sra

ADD COMMENT • link written 4.0 years ago by piet • 1.4k

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