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
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
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