DiffSplice

[Juliaycliu]

I have read the the manual (https://flair.readthedocs.io/en/latest/) and I still have a question about

• diffSplice

In the diffSplice section, it is mentioned, "If there are 3 or more samples per condition, then you can run with --test and DRIMSeq will be used to calculate differential usage of the alternative splicing events between two conditions. " However, I have a two vs three comparison, how could I do? Shall I simply modify drim1 to 5 and drim2 to 2 in this case?

--drim1 The minimum number of samples that have coverage over an
AS event inclusion/exclusion for DRIMSeq testing; events
with too few samples are filtered out and not tested (6).
--drim2 The minimum number of samples expressing the inclusion of
an AS event; events with too few samples are filtered out
and not tested (3).

Thank you!!
Julia

[cafelton]

You could try doing that! You could also try taking the diffSplice output and running a t-test on it. That would be a more conservative approach than running drimSeq. Another approach we've used in the past for 2v2 datasets is running a fishers exact test on every pair and considering events significant if they have p<0.05 in both between conditions pairs and >0.05 in both within conditions pairs. This is my favorite approach with few replicates, but it does become a bit cumbersome with 2v3.