Question: Is there a Faster tool to convert from .SRA files to .Fastq ?
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gravatar for Chen
2.4 years ago by
Chen730
Chen730 wrote:

I download a SRA file from NCBI, with 166G size.

Then I use fastq-dump -I --split-files ./File.sra to convert it to fastq file on a server with 1Tb memory and 10K RPM disk.

With four hours it only generates 400M fastq file, it seems that convering the file will take forever.

To be precise, its converting speed is about 2M/min, which means it needs around 60 days to convert this file...

Nature Publishing Group journals require that DNA and RNA sequencing data is made available through the SRA(http://www.nature.com/authors/policies/availability.html). It does not make sense to upload SRA format if it is so inconvenient.

Is there a better and faster way to convert, or I am using wrong command?

fastq sra ncbi • 1.1k views
ADD COMMENTlink modified 2.4 years ago • written 2.4 years ago by Chen730
2

Check EBI-ENA with the accession number. Get fastq files from them directly without having to mess with SRA data.

ADD REPLYlink written 2.4 years ago by genomax57k

Thanks, this idea is very useful!!

ADD REPLYlink written 2.4 years ago by Chen730

What kind of storage system are you using? Some storage systems that are not tuned for a large amount of random access may be problematic (or at least have been in the past).

ADD REPLYlink written 2.4 years ago by Sean Davis25k

It is hp SAS disk.

ADD REPLYlink written 2.4 years ago by Chen730

A 166 Gb SRA file is huge! What is the compression ratio for SRA to fastq?

Just out of curiosity, what kind of sequencing is it? Genome, ChIP, RNA?

ADD REPLYlink written 2.4 years ago by jotan1.2k

it's next generation sequencing data, hiseq raw reads for genome

ADD REPLYlink written 2.4 years ago by Chen730
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