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Old 06-04-2010, 09:22 AM   #1
Junior Member
Location: Boston

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Default public data sets

So I want to find a public data set of aligned DNA sequencing reads, so that I can compare a workflow I am using on my samples to a control data set. Does anyone know the best way to search for such a thing?

Sorry I am rather new to all this. Any pointers would be appreciated.
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Old 06-04-2010, 01:26 PM   #2
Peter (Biopython etc)
Location: Dundee, Scotland, UK

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I'd grab transcriptome reads for a public genome from the NCBI SRA and align them myself (e.g. with maq or bwa).
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Old 06-08-2010, 02:48 AM   #3
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Location: Southern France

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The Encode project is generating tons of data, including aligned reads.
You can access all this from the UCSC, see for instance the ENCODE Caltech RNA-seq track. More info (well, much more, muchomaas) about other tracks is available in the table browser section, but to download i recommend the ftp: for instance, from this page, the 4 first files are aligned reads from RNA-seq experiments (on hg18).

Now, if at some point you find another public source of already aligned reads, could you please let me know? I am interested in the very same thing.

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