How to estimate the total copy number of genes from FPKM values?

[Pradhaun]

Hello all,

I am using Tophat and cufflinks to estimate the copy number of genes in an organism by comparing to its closely related organism genes. I got a bam and gtf file as a outputs from Tophat and Cufflinks . I tried to view the alignment (Tophat output) file as well as the gtf file in IGV. I can see the FPKM value for every single gene but My question is, how can I know whether these two organisms are closely related? Like for eg., "There are x number of same set of genes present in both the organisms" Or is there any way to know the overall FPKM or copy number?

I am new to this kind of study, am not sure whether my thinking can be applicable or not. So I would appreciate if you can please provide your suggestions...

Thank you,
Pradhaun

[rboettcher]

Cufflinks is designed to output differentially expressed genes, isoforms etc. Therefore, it only gives you a measure of abundance for transcripts / isoforms / etc. from which you can derive the relative expression of a gene and its isoforms.

You should try to look for a tool which fits your analysis plan (for instance, see here: http://seqanswers.com/forums/showthread.php?t=1409).

Nevertheless, I doubt that you can perform a robust CNV analysis via RNAseq, as you will have to distinguish differential gene expression from a CNV and I have no idea how you would do so (I admit that I never tried). Thus, I whould look for SNP-arrays or DNAseq as an analysis method instead.

Best regards