Question: How to calculate differential usage of splice junction
1
gravatar for Anil Kesarwani
3.9 years ago by
United States
Anil Kesarwani80 wrote:

Hi,

Could some body please guide me about how to calculate differential usage of splice junction between two samples. I have read count information for each junction detected from TopHat2 alignment. The samples are in replicates, so P-value and FDR will be needed to select significant differentially used splice junctions.

Could it be so simple that I normalize the splice junction read count by total mapped read and then further normalize with gene expression (FPKM value) (to rule out the altered usage of junction reads was due altered gene expression. Please correct me if i am wrong.

 

 

rna-seq tool • 1.6k views
ADD COMMENTlink modified 3.9 years ago by Antonio R. Franco4.0k • written 3.9 years ago by Anil Kesarwani80
0
gravatar for Antonio R. Franco
3.9 years ago by
Spain. Universidad de Córdoba
Antonio R. Franco4.0k wrote:

Have you give a look to limma (R). ?

Even though it was initially designed for microarray analysis, it can now handle RNA-Seq including splicing

ADD COMMENTlink written 3.9 years ago by Antonio R. Franco4.0k
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