RNA-seq analysis with stranded and unstranded data

[siddha]

Hi,

I have a dataset in which 30 samples are strand specific and 6 are unstranded. Is there any way to analyze these samples together for gene expression? Both sets were sequenced using Illumina Tru Seq. Would greatly appreciate any help.

Thanks

Siddha

[dpryan]

Just include the library-type as a factor in the design.

[super0925]

You could try library-type to determine the pipeline design