[BioC] any package to do gene expression value estimation

[Wei Shi]

Even you map your reads to the transcriptome, you still have the problem of junction read mapping because the annotated transcriptome is unlikely to include all the alternative isoforms of each gene. Those junction reads, which contain exon junction locations that are not included in your transcriptome, can not be mapped if you are not using junction-aware read aligner.

Wei

On Oct 26, 2011, at 9:07 AM, wang peter wrote:

> 
> thx for your reply.
>        but i map those reads to transcripsome, not genome.
> i think i donot need consider the junction.
>        so i care more on the efficiency
>  
> shangao


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