Question: Is there a Faster tool to convert from .SRA files to .Fastq ?
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gravatar for Chen
20 months ago by
Chen590
Chen590 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 • 802 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by Chen590
2

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

ADD REPLYlink written 20 months ago by genomax40k

Thanks, this idea is very useful!!

ADD REPLYlink written 20 months ago by Chen590

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 20 months ago by Sean Davis24k

It is hp SAS disk.

ADD REPLYlink written 20 months ago by Chen590

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 20 months ago by jotan1.1k

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

ADD REPLYlink written 20 months ago by Chen590
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