Converting .sra files to fastq

Question: Converting .sra files to fastq

6.3 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 • 9.1k views

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modified 6.3 years ago by piet • 1.8k • written 6.3 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 6.3 years ago • written 6.3 years ago by Zhaorong • 1.3k

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 6.3 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 6.3 years ago by Ming Tang • 2.6k

6.3 years ago by

Varun Gupta • 1.2k

United States

Varun Gupta • 1.2k 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 6.3 years ago by Varun Gupta • 1.2k

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 6.3 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 6.3 years ago by Linda • 150

6.3 years ago by

piet • 1.8k

planet earth

piet • 1.8k 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 6.3 years ago by piet • 1.8k

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