Alternative splicing analysis, rna-seq
Hello
I took rna-seq data (d. melanogaster, SAM fles) from modencode for two samples (empbryos 0-4 hrs and 4-8 hrs), put it to cufflinks (cuffdiff) and got output with isoforms' RPKM in both samples and genes' RPKM.
I compared the data I got about genes' RPKM to data on flybase.org and found out that they are quite different.
For example, for gene Act79B I got RPKM_1 392.168 and RPKM_2 1184.06 but data on flybase shows that less than 3 for both samples.
What am I doing wrong? Or this comparison is incorrect?
• 3,377 views
•
link
updated
by
Ram
•
written
by
marina-orlova
•
written
by
marina-orlova
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Is it possible to obtain gene description (from gene ids) for D. melanogaster with the biomaRt R pa…
written by antonioggsousa
-
which data is more suitable for Heatmap?
written by star
-
Error about using cummeRbund package to load cuffdiff output data
written by 673422688 •
-
No differential gene expression after tuxedo protocol
written by vinayjrao
-
optimum statistical test to get significance level
written by ashkan
-
Cuffdiff (weird) output
written by rna-seq_researcher •
-
Differential Isoform Expression In Cuffdiff: How Does It Work?
written by gwilymh1000 •
-
Differentially Expressed Genes In Highly Correlated Samples?
written by Pfs
-
Rpkm Or Fpkm For Paired End Data Analyses Of Gene Expression?
written by Nebo •
-
How To Get The List Of Genes Involved In A Biological Process
written by Dejian
I wouldn't assume that the values are comparable. There's more than one way to get at an RPKM value (e.g., do you use raw or normalized counts). Even using different versions of cufflinks will lead to changes in RPKM values.
To add on to Devon, here is the paper on the problem of RPKM and previous discussion on biostar.
So, does it mean that I can't use it for alternative splicing analysis or not?
Thank you for the reply!