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.
What is please exon inclusion level?
Exon inclusion is a measure of the expression (inclusion) of an exon relative to the expression of the gene. It is a useful indicator of alternative splicing when compared between conditions.