Hi all,<br>Is there any way to find out the number of reads aligning to a transcript rather than the FPKM calculated by Cufflinks?<br><br>I&#39;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?<br>
<br>Thanks for your help and providing this great resource,<br>James<br>