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, James
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