count TPM-transcript per million TPM TPM-transcript per million TPM TPM, which stands for Transcript Per Million, is a data item produced during a normilization procedure of RNA-Seq data (i.e. transcription profiling reads produced by nucleic acid sequencing) and corresponds to the count per length of transcript (kb) per million reads mapped. -TPM considers the gene length and sequencing depth for normalization -TPM proposed as an alternative to RPKM due to inaccuracy in RPKM measurement (Wagner et al., 2012) -TPM is suitable for sequencing protocols where reads sequencing depends on gene length -TPM is RPKM scaled by a constant to make sure the sum of all values is 1 million. -TPM (transcript per million) = 1,000,000*θi/(ℓi*c), where c is a constant value, sum_[j](θj/ℓj), sum_[i]TPM=1,000,000 Recommended use: -TPM measure is suited for gene count comparisons within a sample or between samples of the same sample group. -TPM measure is NOT suited for Differential Expression analysis. https://www.biostars.org/p/273537/ http://www.arrayserver.com/wiki/index.php?title=TPM https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html Philippe Rocca-Serra https://github.com/ISA-tools/stato/issues/79 and https://github.com/mcourtot/FAIRPlus_squad2/issues/50 ready for release