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
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
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