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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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?
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