5. If you have multiple conditions for differential AS analysis

For users with multiple conditions (i.e. two drug treated samples versus control, or three different tissue samples), we suggest to run pair-wise comparison of each experimental condition versus the control, respectively.

For this, create two different input folders (i.e. drug1_versus_control and drug2_versus_control) for each of the comparisons and move the corresponding input files into each folder (i.e. move input files for samples under conditions drug_treatment_1 and control to folder drug1_versus_control and input files for samples under condition drug_treatment_2 and control to folder drug2_versus_control, respectively). And then run JUM in each folder, respectively.

JUM output all the AS events with their coordinates as their ID. So it will be convenient for users to compare the differentially spliced AS events among different experimental conditions versus control from the final results (i.e. differential AS splicing brought by drug treatment 1 compared to control versus differential AS splicing brought by drug treatment 2 compared to control).

For users with time course datasets, two options are present. 1) Run pair-wise comparison of each time point dataset to the control and compile the results across time; 2) JUM can also analyze all samples together, based on the users' specific needs. For this please contact me for details.