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vinay052003 05-21-2011 10:05 AM

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?

Thanks.


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