Re: GMOD expression data

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Re: GMOD expression data

Scott Cain
Hi Yasir,

There is a module for storing expression data, but there isn't a dedicated command line tool for storing expression data.  I cc'ed both the Chado and Tripal mailing lists to get input from users for how they deal with expression data like this.  Perhaps you could also flesh out a little what organism you're working with and what sort of data you have.

Scott


On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <[hidden email]> wrote:
Dear Scott,

Thank you for your help on Chado. Is there a chado module for expression data? I want to load my RNAseq expression results on a GMOD website. Could you please point me in the right direction?

Best,
yasir



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Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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Re: GMOD expression data

Yasir Suhail
Hi Scott,

I am working on Brassica napus RNAseq data for one treatment, 2 time points.

I have some syntenic homologs, and pathways of interest of a related species (Arabidopsis). I will be happy with any tools that may provide users with a way to select and visualize the gene expression data and look at genes of interest.

Best,
yasir

On Mon, Nov 2, 2015 at 11:47 AM, Scott Cain <[hidden email]> wrote:
Hi Yasir,

There is a module for storing expression data, but there isn't a dedicated command line tool for storing expression data.  I cc'ed both the Chado and Tripal mailing lists to get input from users for how they deal with expression data like this.  Perhaps you could also flesh out a little what organism you're working with and what sort of data you have.

Scott


On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <[hidden email]> wrote:
Dear Scott,

Thank you for your help on Chado. Is there a chado module for expression data? I want to load my RNAseq expression results on a GMOD website. Could you please point me in the right direction?

Best,
yasir



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research


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Re: [Gmod-tripal] GMOD expression data

Meg Staton-2
In reply to this post by Scott Cain
Hi, Yasir,
There are a number of groups working on this right now; I hope to have an expression data module publicly launched by spring. 

Andrew Farmer and I have discussed the incompatibility of chado with RNASEq expression data - its really designed for microarray data (ie the MAGE module). The current code from my lab will use the MAGE module, but in the long term it would be nice to update the schema.

Meg

On Mon, Nov 2, 2015 at 11:47 AM, Scott Cain <[hidden email]> wrote:
Hi Yasir,

There is a module for storing expression data, but there isn't a dedicated command line tool for storing expression data.  I cc'ed both the Chado and Tripal mailing lists to get input from users for how they deal with expression data like this.  Perhaps you could also flesh out a little what organism you're working with and what sort of data you have.

Scott


On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <[hidden email]> wrote:
Dear Scott,

Thank you for your help on Chado. Is there a chado module for expression data? I want to load my RNAseq expression results on a GMOD website. Could you please point me in the right direction?

Best,
yasir



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

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Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

864-506-4515 Mobile





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Re: [Gmod-tripal] GMOD expression data

Scott Cain
Hi Meg,

So what do you do now, store the data in a custom schema, or do you shoe-horn it into Chado?  I assume the goal is to gather information about the experiment and then link it to an external data file (presumably BAM or BigWig).

Thanks,
Scott



On Tue, Nov 3, 2015 at 7:34 AM, Meg Staton <[hidden email]> wrote:
Hi, Yasir,
There are a number of groups working on this right now; I hope to have an expression data module publicly launched by spring. 

Andrew Farmer and I have discussed the incompatibility of chado with RNASEq expression data - its really designed for microarray data (ie the MAGE module). The current code from my lab will use the MAGE module, but in the long term it would be nice to update the schema.

Meg

On Mon, Nov 2, 2015 at 11:47 AM, Scott Cain <[hidden email]> wrote:
Hi Yasir,

There is a module for storing expression data, but there isn't a dedicated command line tool for storing expression data.  I cc'ed both the Chado and Tripal mailing lists to get input from users for how they deal with expression data like this.  Perhaps you could also flesh out a little what organism you're working with and what sort of data you have.

Scott


On Mon, Nov 2, 2015 at 10:55 AM, Yasir Suhail <[hidden email]> wrote:
Dear Scott,

Thank you for your help on Chado. Is there a chado module for expression data? I want to load my RNAseq expression results on a GMOD website. Could you please point me in the right direction?

Best,
yasir



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     <a href="tel:216-392-3087" value="+12163923087" target="_blank">216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------

_______________________________________________
Gmod-tripal mailing list
[hidden email]
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--
Margaret Staton
Assistant Professor
Department of Entomology and Plant Pathology
370 PBB, 2505 EJ Chapman Drive
Knoxville, TN 37996-4560

<a href="tel:864-506-4515" value="+18645064515" target="_blank">864-506-4515 Mobile







--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

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