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Has anybody gotten this to work using windows? If not, are there any ways to convert sra to fastq for someone on a windows OS? It seems that Galaxy has nothing regarding sra file formats.
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I think I got it
I went back to NCBI website and found a ncbi sra toolkit designed for 32 bit windows os. It seems to be working now. -
Use SRA to do conversion?
A few months ago Stephen Taylor suggested using the SRA's conversion itself:
The way I got round this was let the SRA website do the conversion. So just paste in the URL in the upload screen:
Where SRRXXXXXX is the archive of interest, and it downloads Sanger FASTQ sequences to Galaxy.
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Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
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