Hi all,


I have about 30 libraries of SBS data (millions of 20nt tags) to analyze the differences between or among different libraries, and lots of these tags are in intergenic regions. 

For gene regions, I think I can use DESeq or EdgeR to analyze the DE genes. But it seems that  DESeq or EdgeR can only deal with two samples, is there any package to compare multiple samples one time. For example, to find genes expressed highly in one or some libraries but not in other libs.

But for intergenic tags, I think first I should use some peak detection package to find peak in intergenic, then treat these peaks as genes to find DE regions. 

Is there any peak detection package for NGS? and package for DE analysis among multiple libs? 

Thank you!

Regards, 
Xiaohui

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