Hi all,
Is there any way to find out the number of reads aligning to a transcript
rather than the FPKM calculated by Cufflinks?

I'm also interested in obtaining summary statistics for mapping analyses or
RNA-Seq data, such as % of  reads aligned, % uniquely aligned, mapped to
exons, introns, etc.  Is there a tool that would provide a summary table
with this information?

Thanks for your help and providing this great resource,
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