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Dear @hartleys ,
Thanks you for putting together a great bit of software and continuing to support it.
I have been using JunctionSeq on some RNA-seq data happily for a while but recently have come into a problem with some of my pairwise tests. I have a time series over 3 time points with 2 conditions that I am comparing in a pairwise manner, as well as doing as one.
When I compare the two conditions at a time point JunctionSeq runs without error but when I do across time points with the same condition I am getting a script out of bounds error. Understandably there will be a lot more differences over time compared to between the conditions as the conditions are related here.
I have tried to use method.dispFit='local', and nCores =1 to overcome fitting errors but still get this:
If you have any suggestions they would be most appreciated. I have 4/5 biological replicates per condition per time point.
Below is the output of the command I am using :