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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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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The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...07-08-2024, 03:19 PM
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