Question: Comparing Gene Expression From Strand-Specific Library And Unstranded Library In Rnaseq
1
gravatar for camelbbs
4.5 years ago by
camelbbs610
China
camelbbs610 wrote:

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.

rnaseq strand • 1.3k views
ADD COMMENTlink modified 4.5 years ago by Nicolas Rosewick5.7k • written 4.5 years ago by camelbbs610
2
gravatar for Nicolas Rosewick
4.5 years ago by
Belgium, Brussels, Université Libre de Bruxelles / Université de Liège
Nicolas Rosewick5.7k wrote:

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.

ADD COMMENTlink written 4.5 years ago by Nicolas Rosewick5.7k
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