[DAS] Bam file support in GenoPub DAS/2 -> IGB

Thu Nov 25 16:31:59 UTC 2010

Hello Thomas,

FYI. Finally have this up and running.  -cheers, D

------ Forwarded Message
From: David Nix <david.nix at hci.utah.edu>
Date: Wed, 24 Nov 2010 19:58:33 -0700
To: Brett Milash <brett.milash at hci.utah.edu>, Ying Sun <Ying.Sun at hci.utah.edu>, Gholson Lyon <Gholson.Lyon at hsc.utah.edu>, Sean Tavtigian <Sean.Tavtigian at hci.utah.edu>, Russell Bell <Russell.Bell at hci.utah.edu>, Barry Moore <barry.moore at genetics.utah.edu>, M Hobbs <M.Hobbs at hsc.utah.edu>, Reid Robison <Reid.Robison at hsc.utah.edu>, Richard Clark <clark at biology.utah.edu>, Tonya DiSera <Tony.DiSera at hci.utah.edu>, Karin Chen <karin.chen at hsc.utah.edu>, Bradley Katz <Bradley.Katz at hsc.utah.edu>, Brenda Bass <bbass at biochem.utah.edu>, "W. Evan Johnson" <evan at stat.byu.edu>
Conversation: Bam file support in GenoPub DAS/2 -> IGB
Subject: Bam file support in GenoPub DAS/2 -> IGB

Hello Folks,

I've finally worked out what I believe are all the bugs and have enabled bam alignment file support for GenoPub DAS/2 distribution to IGB. (IGB currently supports local desktop BAM file loading.)

You'll have to use http://bioserver.hci.utah.edu/IGB/igb_exe.jar or a build off the current head.  IGB 6.4 won't work since I had to modify a critical utility.  I'll switch over the web start links in a couple weeks after running some more tests. If you want to install the modified server download the archive from http://bioserver.hci.utah.edu/IGB/ das2server-genopub_0.2.zip .

To upload bam files use the Picard tools (http://picard.sourceforge.net) to sort your bam file by coordinate, build an index, and validate both.  Then upload both the xxx.bam and it's corresponding xxx.bam.bai index file simultaneously into the same Annotation in GenoPub.  Note, the C based SamTools seem to generate bam and bai files that don't always pass the java based Picard validation so be sure to run the Picard ValidateSamFile app before uploading to GenoPub.

Let me know if you run into any bugs or odd behavior.

-cheers, D

[cid:3373522319_21881239]
------ End of Forwarded Message

[DAS] 1.6 draft 7

Thomas Down thomas.a.down at gmail.com
Thu Sep 23 10:44:05 EDT 2010
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Hi David,

Just getting in touch to let you know that we're very interested in getting
big piles of sequencing data onto genome browsers, and are certainly
interested in alternative formats.  My current thoughts are that -- at least
for what we're doing -- a slightly more concise XML schema, plus richer
control of server-side summarization/binning (think maxbins++) might be the
sweet spot, but very interested to see other options as well.

Also, just to check... are you currently gzipping your DAS XML?  This makes
a *huge* (at least 10-fold, potentially more) difference, and while I agree
it's still not quite optimal, this has got us a long way so far.  It's
possible to negotiate compression purely in the HTTP layer (using the
Accept-Encoding header), so doesn't necessarily impact the DAS spec at all.

Best wishes,

               Thomas.

On Wed, Sep 22, 2010 at 9:33 PM, David Nix <David.Nix at hci.utah.edu> wrote:

> Bugger, that's unfortunate.  Without alternative formats, it is impossible
> to distribute genomic data from next generation sequencing and microarray
> experiments in a timely manner.  Even then, the data transfer is very slow
> due to the <2MB/s bandwidth limitation.
>
> I wonder if folks should be encouraged to use DAS/2 for genomic data
> distribution and DAS/1 for everything else?  There seems to be a great
> reluctance to add alternative formats to DAS/1.  I can understand the
> advantages of having a standardized data distribution format.  Unfortunately
> this won't work for us, even compressed, DAS GFF XML is about 100x larger
> than some of the other binary genomic data formats such as bar and useq.
>
> I'm afraid DAS is going to get left behind as other data distribution
> models are adopted that can accommodate the ever growing density of genomic
> data.
>
> What do you think?
>
> -cheers, D
>
> On 9/22/10 10:51 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
>
> Hi David,
>
> It is not part of DAS 1.6 but was discussed at the DAS workshop. During the
> workshop we had some discussion on the topic and came up with a couple of
> sensible proposals for an extension to 1.6 to cover it. If my memory serves
> me we agreed on an outline proposal, and there is a write up on
> http://www.biodas.org/wiki/DAS1.6E (courtesy of Gregg? Is that correct?)
> but as far as I know there are no implementations as yet.
>
> Cheers,
> Andy
>
> On 22 Sep 2010, at 17:17, David Nix wrote:
>
> > Hello Andy,
> >
> > I'm looking at the latest and trying to find out if alternative file
> formats were added to 1.6?  Can one respond to DAS/1 queries with binary
> data formats or is it still XML?  If the later, any time frame for when this
> will be added?
> >
> > -cheers, D
> >
> > --
> > David Austin Nix, PhD | Bioinformatics Shared Resource | Huntsman Cancer
> Institute | 2000 Circle of Hope | SLC, UT 84112 | Rm: 3165 | Vc:
> 801.587.4611 | Fx: 801.585.6458 | david.nix at hci.utah.edu | Skype/iChat:
> LiveNix | WebSite: http://bioserver.hci.utah.edu | DAS/2:
> http://bioserver.hci.utah.edu:8080/DAS2DB/genome
> >
> >
> >
> > On 9/22/10 9:44 AM, "Andy Jenkinson" <andy.jenkinson at ebi.ac.uk> wrote:
> >
> > Hi all,
> >
> > I have updated the 1.6 specification to draft 7 in light of recent
> discussions on the list:
> > 1. All features in a parent/part hierarchy must be returned if any
> overlap a query segment.
> > 2. The alignment command is back to extension status, in anticipation of
> a revamp (see the 1.6E page on the wiki).
> >
> > Also in this draft is a previous change that was missed: the start and
> end attributes of a SEGMENT element in the features, types and entry_points
> commands are now optional. This makes it possible for servers without access
> to detailed information about the segments they are annotating to comply
> with the specification. Previously, it was impossible for such servers to
> respond in a compliant fashion to requests in which the client does not
> specify a start/end position.
> >
> > If my understanding is correct, no further changes to the specification
> are anticipated which means we can consider this the final draft...
> >
> > See here for details:
> > http://www.biodas.org/wiki/DAS1.6
> >
> > Cheers,
> > Andy
> > _______________________________________________
> > DAS mailing list
> > DAS at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/das
> >
>
>
>
> _______________________________________________
> DAS mailing list
> DAS at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/das
>
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