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Question: Galaxy and transgenic organisms
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gravatar for dandrew
3.3 years ago by
dandrew • 10
United States
dandrew • 10 wrote:

Greetings,

I am using Galaxy to analyze some RNA-seq time-course experiments. These exp's involve monitoring the induction of a viral transgene (and other genes that are coordinately induced) when compared to uninduced controls in a transgenic organism.

How do I go about adding my transgene and promoter to the genome.fa and genes.gtf files so that its induction is visible in the results? 

Do i even need to do this to see this data?

Can you recommend some references that address the issue of using Galaxy in the analysis of RNA-seq data from transgenics? 

Cheers,

dandrew
rna-seq galaxy • 781 views
ADD COMMENT • link •
modified 3.3 years ago by Bjoern Gruening ♦ 5.1k • written 3.3 years ago by dandrew • 10
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gravatar for Bjoern Gruening
3.3 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Maybe you can create a new organism that includes all genes that will be induced during your experiement? You could integrate this artificial genome in a next step into Galaxy and proceed with a standard RNA-seq pipeline.
 
ADD COMMENT • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k

Thanks for your reply,

All i need to add is one gene seq. The others will be native genes that react to the induction of the transgene and will be simple to follow. Can you give me some more explanatory information on your statement ,"integrate this artificial genome in a next step into Galaxy"? I do not understand these concepts .

Thanks,

dandrew

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ADD REPLY • link written 3.3 years ago by dandrew • 10

This is called custom genome. Have a look at this wiki page: https://wiki.galaxyproject.org/Learn/CustomGenomes

But actually, you don't need this. Every tool that you need can take a fasta file as reference genome. So you are save without this.

ADD REPLY • link written 3.3 years ago by Bjoern Gruening ♦ 5.1k
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