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I am trying to use scripture now. Yes , it needs some pre-processing of tophat output files, including combining, sorting, and indexing. I have just finished the pre-processing right now.
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Originally posted by Gangcai View PostYou can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/
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You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/
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Check out http://useq.sourceforge.net/ and the user guide describing differential transcriptome analysis http://useq.sourceforge.net/usage.html .
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advanced tools in RNA-seq analysis
Hello All,
My boss asked me to use at least three most commonly used RNA-seq analysis software/tools to process some data (paired end, 75 bp, human) and compare them. I know that Tophat/Cufflinks is a very powerful and popular pipeline -- from mapping to assembly.
What else? Could anybody give me some suggestions?
Thanks!!
IrisLast edited by IrisZhu; 07-30-2010, 12:50 PM.Tags: None
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