[GET-dev] where do I get raw data ?

[Erik Garrison]

Are there any sequence read datasets available in addition to the GFF files?

-Erik

On Wed, Dec 22, 2010 at 2:55 PM, Madeleine Price Ball <meprice at gmail.com>wrote:

> Sorry, it's been changing as we update the genome analysis methods.
>
> If you click on any of the PGP genomes that say "with indel and
> coverage" it should have indel and coverage information in the
> downloadable gff data. For example:
>
>
> http://evidence.personalgenomes.org/genomes.php?display_genome_id=65711e3d6829f08c2f8aeeaf06b67b4d2c744e38
>
> If you click on "Source data: download GFF (115 MB)" you'll get a file
> called "PGP1_\(George_Church\)_with_indel_and_coverage.gff" but ...
> it's actually gzipped. Sorry. You'll probably want to do:
>
> mv PGP1_\(George_Church\)_with_indel_and_coverage.gff
> PGP1_\(George_Church\)_with_indel_and_coverage.gff.gz
>
> FWIW - there's a fix for this bug here, maybe Tom can pull it to the main
> site:
>
> https://github.com/madprime/get-evidence/commit/129e510318bd5381d86cd6ab1e9aca5976bd1c46
>
> I've made a write up for how indels and coverage are marked here:
> http://evidence.personalgenomes.org/guide_upload_and_source_file_formats
>
> On Tue, Dec 21, 2010 at 8:43 AM, Leon Peshkin <peshkin at gmail.com> wrote:
> > Hello!
> >
> > Could someone help me with a pointer to PGP-10 raw data files, that is
> more
> > than list of SNPs.
> > I am interested to get a pretty short (few thousand nucleotide) chunks to
> > compare across individuals,
> > but it might contain deletetions in some.
> >  Sasha mentioned that data is available from
> > http://evidence.personalgenomes.org/genomes
> > but I do not see any mention of "coverage and indels" at the page.
> > There is a link to http://evidence.personalgenomes.org/download
> >  which is linked to the SQL dump and flat tsv file, but not BAM or SAM,
> so I
> > am somewhat confused.
> >
> > -Leon
> >
> >
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> > http://lists.freelogy.org/mailman/listinfo/get-dev
> >
> >
>
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