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
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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