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Old 08-22-2010, 07:55 AM   #1
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Default Comparing Transcriptomes

Hey, I'd like to compare the upregulation / downregulation of multiple transcriptomes (~ 5) when exposed to the same environmental stimulus. What I'm wondering is whether there are existing perl scripts / software programs to do this. Does anyone know? I'm willing to cook 'em up but don't want to re-make the wheel if I don't have to. Thanks.
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Old 08-26-2010, 12:23 AM   #2
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In order to stimulate discussion related to your question it would be helpful to know more details.

Describe your data: sequencing platform? Number of reads per library? Paired or single end? Read length?

Experimental design: You say five conditions, but are paired comparisons available (treated vs untreated)? Do you have biological replicates?

Analysis goals? Expression analysis only? Gene level only or alternative expression as well?
malachig is offline   Reply With Quote

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