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Old 05-21-2011, 10:05 AM   #1
Location: Atlanta, US

Join Date: Jan 2010
Posts: 59
Default Isoform quantification using RNA-seq

I have RNA-seq data from 454 sequencing technology and I want to quantify the expression levels of the splice variants. The first choice available is Cufflinks but that works only for short reads such as from Illumina.
I was going through their algorithm and it sounds a bit complicated to implement. Has anyone done that before? Any suggestions for another program/algorithm for long RNA-seq reads?

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