What is the difference between Cufflinks and other packages

[adrian]

Hi:

I have naive question and hope I could get an answer here.

What is the difference between Cufflinks and other softwares such as edgeR, ERANGE.

My aim is :

I have RNA-Seq data from 5 cancer samples and 5 normal samples. (10 are different people).

I want to have :
a. alternative splicing events and novel isoforms.
b. Gene expression differences between known transcripts.

cufflinks - can identify novel transcripts (through assembly) and estimates abundance of transcripts and computes differential RNA levels.


edgeR - is an R package that can compute differential expression of known transcripts between 5 cancer and 5 normal samples.
edgeR cannot assemble novel transcripts and calculate their abundance.


question:

Can Cufflinks give me the differential expression between known and novel transcripts between 5 cancer and 5 normals. And can this be comparable to edgeR. The methodology is different for both.

Cuffdiff - Although cuffdiff is designed to compare relative abundance between samples, can we define [T1,T2,T3,T4,T5] and [N1,N2,N3,N4,N5] samples as two blocks. I am not sure how cuffdiff will compare 5 normals and 5 tumors.



Any help is deeply appreciated as I am very much confused. May be I have the gene expression (LIMMA) hangover !

thank you.

Adrian

[AdamB]

The current version of Cufflinks supports replicates for comparison.

[frozenlyse]

You could perform novel transcript assembly using cufflinks, merge with known genes using cuffcompare and then use the resulting annotation as gene definitions to use in an edgeR workflow