SRA Toolkit overview
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SRA (Sequence Read ArchiveSequence Read Archive) is an NCBI-defined interchange format for NGS data. The idea is that before submitting your data to NCBI, you convert whatever format it is in (fastq, bam, etc.) to SRA format using one of the "load" tools. Then, the data can be downloaded from NCBI by anyone and extracted in one of a number of different formats as desired (ABI csfasta/qual, fastq).
While this sounds like a great idea (someone else taking care of format interchange issues for you!), the toolkit is no longer being actively developed except for bug fixestookit is somwhat obscure and quirky, so in practice it is used mostly to download fastq files from NCBI. However there is a lot of interesting data out there that's only available as SRAs so it is worthwhile knowing how to use it.
For example, you have aligned a ChIP-seq dataset to hg19 and have a .bam file. You want to upload the data to NCBI. You use the bam-load tool:
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Finding data
Submissions for a publication publication generally have the form SRPnnnn SRPnnnn, with all the data under an accession SRAnnn accession SRAnnnn (the n's have no relation to one another). Data is organized by experiment (SRXnnnnexperiment (SRXnnnn) and sequencing run (SRRnnnn run (SRRnnnn).
The SRA search home page is where to start looking.
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Find and download RNAseq data from run SRR390925, of experiment SRX112044, publication SRP009873. Copy the file to your home directory on Lonestar Lonestar5 at TACC then extract the data in fastq format.
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