is about has_specified_input is_specified_output_of gene expression paired-end library RNA-seq assay count FPKM-fragments per kilobase of transcript per million fragments mapped FPKM FPKM, which is the expected fragments per kilobase of transcript per million fragments mapped is a metric used to report transcript expression event as generated by RNA-Seq using paired-end library. The calculated value results from 2 types of normalization, one to take into account the difference in reads counts associated with transcript length (at equal abundance, longer transcripts will have more reads than shorter transcripts) , (hence the 'per kilobase of transcript') and the other one to take into account different sequencing depth during distinct sequencing runs (hence the 'per millions mapped fragment'. The metric is specifically produced by cufflink software. Recommended use: -FPKM measure may be used for gene count comparisons within a sample. -FPKM measure is NOT suited for between sample comparisons. -FPKM measure is NOT suited for Differential Expression analysis. The definition of FPKM has been modified in October 2019 to reflect the possible uses as detailed in https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html and distinguish more clearly FPKM from measures such as TPM Orlaith Burke Alejandra Gonzalez-Beltran Philippe Rocca-Serra adapted from: http://seqanswers.com/forums/showthread.php?t=3254 and from http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html and from https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html pending final vetting