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Say I have one gene of interest. Based on Ensemble annotation, this gene has 10 isoforms. I want to use cufflinks to estimate the expression of these 10 isoforms and test for differential usage of these 10 isoforms between my case and control samples. In other words, I want to compare whether the relative expression of these 10 isoforms are the same or not between my case and control.
Seems cufflinks only compare a subset of the isoforms of a gene (results in splicing.diff and promoters.diff) but not all of them?
I am also a bit confused how does cufflinks define primary transcript? I can find definition in your supplementary text, but for a particular gene I am interested, can I tell which transcript is primary by the annotation in GTF file?
Thanks a lot.
Seems cufflinks only compare a subset of the isoforms of a gene (results in splicing.diff and promoters.diff) but not all of them?
I am also a bit confused how does cufflinks define primary transcript? I can find definition in your supplementary text, but for a particular gene I am interested, can I tell which transcript is primary by the annotation in GTF file?
Thanks a lot.