For cufflinks, I know that cuffdiff can perform statistical test for identifying differential expressed genes. And I also know that there are several other tools could conduct statistical analysis for Rna-seq data, like DEseq.
But, is it reasonable to do Rna-seq like this:
1. Tophat to align the data
2. Cufflinks to get normalized expression values (FPKM).
3. combine the FPKM values from different samples
4. perform statistical test use the method implemented in Genechips (Affy).
If not, what are the disadvantages to make it impossible? Thanks.
But, is it reasonable to do Rna-seq like this:
1. Tophat to align the data
2. Cufflinks to get normalized expression values (FPKM).
3. combine the FPKM values from different samples
4. perform statistical test use the method implemented in Genechips (Affy).
If not, what are the disadvantages to make it impossible? Thanks.
Comment