Comparing Gene Expression From Strand-Specific Library And Unstranded Library In Rnaseq

Question

[camelbbs]

As I know, the strand-specific and unstranded library have different counting method, so does that make sense to compare the gene expression (rpkm or rpm) from the strand-specific library and from unstranded library? If yes. which normalization method is better for this. Thanks.

Answer 1

[Nicolas Rosewick]

I think you could use a multifactor design with DESeq (R - bioconductor) by specifying a design matrix like that :

Sample    condition    library
A        untreated    unstranded
B       untreated    unstranded
C       treated     unstranded
D       treated     unstranded
E       untreated    stranded
F        untreated    stranded
G        treated     stranded
H        treated     stranded

and with your count matrix :

cdsFull = newCountDataSet( countTable, designMatrix )

after that follow DESeq manual at "Multi Factor Designs" section. http://bioconductor.org/packages/release/bioc/html/DESeq.html

I think edgeR has also this type of feature.