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Fragments Per Kilobase of transcript per Million mapped reads (FPKM) is a simple expression level normalization method. The FPKM normalizes read count based on gene length and the total number of mapped reads.

Transcription is the first step in gene expression. It involves copying a gene's DNA sequence to make an RNA molecule. Transcription is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand (using a DNA strand as a template).

Specifically, gene expression is controlled on two levels. First, transcription is controlled by limiting the amount of mRNA that is produced from a particular gene. The second level of control is through post-transcriptional events that regulate the translation of mRNA into proteins.

For most intents and purpose TPM is superior to CPM (at least for short read RNA-seq; where the length of a given transcript affects the number of reads produced from said transcript). However, CPM should give comparable results to using TPM. In your case, I would try both and compare the results. Use TPM.

When you use TPM, the sum of all TPMs in each sample are the same. This makes it easier to compare the proportion of reads that mapped to a gene in each sample. In contrast, with RPKM and FPKM, the sum of the normalized reads in each sample may be different, and this makes it harder to compare samples directly.

When you use TPM, the sum of all TPMs in each sample are the same. This makes it easier to compare the proportion of reads that mapped to a gene in each sample. In contrast, with RPKM and FPKM, the sum of the normalized reads in each sample may be different, and this makes it harder to compare samples directly.