Is there any way I can get exon inclusion levels from cufflinks. I have different kinds of RNA-seq data with variable read length which we get after trimming. There exists a tool called splicetrap which can be used for calculating exon inclusion levels but It can not take reads which have differing lengths or and It only works on Illumina data not ABI-solid data. I have certain datasets where mrna-seq data is ABI-solid data.
I think the main confounding factor is that many exons belong to exclusive transcript isoforms i.e. exons are defined at the transcript isoform level. You might have to use something like the Union Intersection model or some other approach such as with the deprecated 'canonical exons'. Alternatively, you can use splice junctions provided you have good read depth and wide coverage. See the section titled Analysis of AS and transcript levels by RNA-seq in Saltzman, Arneet L., Qun Pan, and Benjamin J. Blencowe. "Regulation of alternative splicing by the core spliceosomal machinery." Genes & development 25.4 (2011): 373-384.