filtering pre-mRNA

[chrisbala]

Does anyone know any handy tools for filtering pre-mRNA/background/genomic DNA reads from an Illumina RNA-seq dataset. (in my case 75bp, single end)

I'm thinking something along the lines of setting some threshold of expression relative to the adjacent exons. Ideally this would not exclude reads that fall into undescribed exons. (In other words I still want to be able to predict transcripts).

I know there is a parameter in Cufflinks aimed at dealing with this but I have not had much luck with it so far.

Thanks!