Comparing Transcriptomes

poregide · 08-22-2010, 07:55 AM

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.

malachig · 08-26-2010, 12:23 AM

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?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
bacterial transcriptomes	sdantoft	RNA Sequencing	3	04-17-2011 11:14 PM
RNA-Seq: Sequencing transcriptomes in toto.	Newsbot!	Literature Watch	0	02-08-2011 03:00 AM
de novo assembly of transcriptomes	EMeyer	Bioinformatics	12	09-28-2010 12:21 AM
wheat transcriptomes	Triticum	RNA Sequencing	14	12-09-2009 05:38 AM
Mapping transcriptomes by RNA-Seq	MAS_KSA	Literature Watch	0	06-28-2008 04:55 AM

08-22-2010, 07:55 AM	#1
poregide Junior Member Location: us Join Date: Aug 2010 Posts: 2	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.

08-26-2010, 12:23 AM	#2
malachig Senior Member Location: WashU Join Date: Aug 2010 Posts: 117	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?