advanced tools in RNA-seq analysis

[IrisZhu]

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!!

Iris

[ECO]

Might I suggest: http://seqanswers.com/wiki/Special:BrowseData

[Nix]

Check out http://useq.sourceforge.net/ and the user guide describing differential transcriptome analysis http://useq.sourceforge.net/usage.html .

[IrisZhu]

Very helpful!
Thank you guys.

[Gangcai]

You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/

[IrisZhu]

You can try scripture for assembly also : http://www.broadinstitute.org/software/scripture/

Thanks! Have you ever used it? Seems it requires some pre-processing of Tophat output files.

[Gangcai]

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.