Dear all,
I am using cufflinks and cuffdiff to detect different isoforms of gene from some CAGE data. I got very few number of isoforms. I expected to find much more. What is the parameters that you think I should change and play with in order to detect all possible isoforms.
Note: I have two groups of samples, each group has 5 biological replicates.
I am using cufflinks and cuffdiff to detect different isoforms of gene from some CAGE data. I got very few number of isoforms. I expected to find much more. What is the parameters that you think I should change and play with in order to detect all possible isoforms.
Note: I have two groups of samples, each group has 5 biological replicates.
