Monthly Archives: December 2015


NCBI’s fastq-dump has to be one of the worst-documented programs available online. The default parameters for fastq-dump are also ridiculous and certainly not what you want to use. They also have absolutely required parameters mixed in with totally optional parameters, and so you have no idea what is required and what is optional. Here, we take a look at some of the options and hopefully help you decide which parameters to run.

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SRA Metadata

The sequence read archive (aka short read archive) SRA metadata is complex! This is a brief guide to help you navigate it.

One key thing to remember is that:

A project (SRP) has one or more samples. However, projects are in the table called study.
A sample (SRS) has one or more experiments (SRX).
An experiment has one or more runs (SRR).


What you really want are the runs, and this is how you can get them!

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