Multiple assemblies and chado group module

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Multiple assemblies and chado group module

Siddhartha Basu
Hi,
I am trying to model multiple genome assemblies in chado, particularly in my
case multiple genome sequences of the same strain. So, i thought about
a grouping entry and tried to use the group module to represent that.
This is what i have thought roughly so far. Create a grpmember entry to
represent the assembly, rest of the data could go to the grpmemberprop
table. Then link the top level the features(chromosome, supercontig etc)
through feature_grpmember and another one through the organism_grpmember
tables.
Its does seem very simple, intuitive and straight forward to me and
maybe i am missing out on something in my understanding. I am not sure
how to use grp table or what kind data/model would fit in this case.
So, please let me know if i am going the wrong way, any other
suggestions, ideas.
As a side note, here is a previous similar discussion(group module
didn't exist at that time)
http://generic-model-organism-system-database.450254.n5.nabble.com/Guidance-on-loading-multiple-assemblies-feature-naming-etc-td4299131.html
that did mention the grouping concept and use of analysisfeature
table(maybe possible alternative).

thanks,
-siddhartha




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Re: Multiple assemblies and chado group module

Karl O. Pinc
On Tue, 20 Jan 2015 16:49:49 -0600
Siddhartha Basu <[hidden email]> wrote:

> Hi,
> I am trying to model multiple genome assemblies in chado,
> particularly in my case multiple genome sequences of the same strain.

We are doing multiple high throughput
genotyping analysis of different individuals.
You may find our approach relevant.
See:

http://papio.biology.duke.edu/babase_chado_html/chado-vcf-load-ref.html


Karl <[hidden email]>
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Re: Multiple assemblies and chado group module

Siddhartha Basu
Hi Karl,
Thanks for the link, really appreciate.

-siddhartha


On Wed, 21 Jan 2015, Karl O. Pinc wrote:

> On Tue, 20 Jan 2015 16:49:49 -0600
> Siddhartha Basu <[hidden email]> wrote:
>
> > Hi,
> > I am trying to model multiple genome assemblies in chado,
> > particularly in my case multiple genome sequences of the same strain.
>
> We are doing multiple high throughput
> genotyping analysis of different individuals.
> You may find our approach relevant.
> See:
>
> http://papio.biology.duke.edu/babase_chado_html/chado-vcf-load-ref.html
>
>
> Karl <[hidden email]>
> Free Software:  "You don't pay back, you pay forward."
>                  -- Robert A. Heinlein
>
> ------------------------------------------------------------------------------
> New Year. New Location. New Benefits. New Data Center in Ashburn, VA.
> GigeNET is offering a free month of service with a new server in Ashburn.
> Choose from 2 high performing configs, both with 100TB of bandwidth.
> Higher redundancy.Lower latency.Increased capacity.Completely compliant.
> http://p.sf.net/sfu/gigenet
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
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Re: Multiple assemblies and chado group module

Karl O. Pinc
On Mon, 26 Jan 2015 10:13:03 -0600
Siddhartha Basu <[hidden email]> wrote:

> Hi Karl,
> Thanks for the link, really appreciate.

Note that we have not confirmed that chado-vcf-load
actually works.  I've had to add a couple of indexes
to get it to perform and the analysis of the
program is ongoing.




Karl <[hidden email]>
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