Differential Splicing using perind.counts.gz file

[zhangpicb]

Dear @danielnavarrogomez @zhanxw @tfenne @ddpinto @hmontenegro

Thanks for the great tool！

I want use leafcutter Differential Splicing function,and follow the step described in Differential Splicing.

Because Control-Dieaseas data from different study.All control sample from study1,and all disease sample from study2.
We suppose a batch effect influences the expression of a gene. Such batch effect will influence the quantification of each intron in the same direction.Taking the ratio between a intron and its intron cluster effectively cancels out the batch effect.

But Step 3. Differential intron excision analysis use perind_numers.counts.gz ,not the leafcutter ratio file perind.counts.gz file.
This step make me confusing.

Thanks in advanced!