Whenever it comes to analyzing RNA-seq experiments, there is a need for comparing expression data at a quantitative level. Consider a scenario where samples were taken from different conditions and subjected to Illumina sequencing. Whether those samples were multiplexed or sequenced on a single lane each, one generally gets a different number of raw reads from each sample, refelcting experimental and technical biases inherent in the RNA-seq protocols. Various measures for normalization of RNA-seq samples have been proposed, the most widely used being RPKM (reads per kilobase per million). While RPKM tries to account for different sequencing depth by normalizing by the number of reads sequenced in a specific sample, divided by 10^6, this very step causes a systematic bias, as has been shown here:
The central point of these papers is to work out an alternative measure for RNA-seq expression abundance that resembles as closely as possible the relative molar concentraction (rmc) of each RNA species present in a sample. It is easy to see that the average rmc across genes has to be a constant that only depends on the number of genes mapped in an RNA-seq experiment.
One example of measures that fulfills the invariant average criterion is Transcript per million (TPM), being defined as
where t_g is a proxy for the number of transcripts that can be explained by a certain number of mapped reads and T is the sum of all t_g over all genes. If one is interested in mRNA abundance, the average TPM - and thus the average rmc is inversely proportional to the number of features present in a reference annotation.
Practically, TPM values for individual genes can be computed from read count tables, ie. tables that give the number of reads overlapping a specific gene. Typical programs for obtaining read count tables are htseq-count or multiBamCov (see bedtools multicov).
I have recently implemented normalize_multicov.pl, a tool for computing normalized RNA-seq expression in terms of TPM from multicov files. It is part of the ViennaNGS Perl Modules for NGS analysis and very easy to use: Just provide it the output of a bedtols multicov run on your data as well as the read length used for sequencing your samples and get back a normalized multicov file of your samples in terms of TPM. That's all ...