strand specific RNA-seq mapping

qqtwee · 05-09-2012, 05:54 AM

Does anyone know how do mapping for strand specific RNA-seq data? which tools can work well? what the parameter of tools for strand specific infomation of RNA-seq data?
Looking forward to your answer.
Thank you very much! Best wishes!

dadada4ever · 07-10-2012, 10:23 PM

Tophat is much preferable I guess. Because it can align RNA-Seq reads with juntion, as well as the --library-type parameter to tackle with strand-specific library.

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05-09-2012, 05:54 AM	#1
qqtwee Member Location: Beijing Join Date: Feb 2011 Posts: 16	strand specific RNA-seq mapping Does anyone know how do mapping for strand specific RNA-seq data? which tools can work well? what the parameter of tools for strand specific infomation of RNA-seq data? Looking forward to your answer. Thank you very much! Best wishes!

07-10-2012, 10:23 PM	#2
dadada4ever Member Location: Beijing Join Date: Mar 2010 Posts: 18	Tophat is much preferable I guess. Because it can align RNA-Seq reads with juntion, as well as the --library-type parameter to tackle with strand-specific library.