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Old 08-21-2012, 12:30 PM   #1
madav
Junior Member
 
Location: Leuven

Join Date: May 2012
Posts: 2
Default Defining a transcriptome

Hi,

I'm working with CLC to map Illumina paired end data from various plant varieties against either a CDS set or an annotated genome, depending on the species, and so to determine tissue transcript expression levels.

Clearly a few mapped reads cannot constitute true transcript expression, so my question is whether there is a generally accepted cutoff filter, based on RPKM or something else that can be used to define the transcriptome for that sample?

thanks in advance
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