RPKM - Reads per kilo base per million mapped reads Normalization for comparing gene coverage values. RPKM corrects differences in both: sample sequencing depth and gene length. RPKM - Reads per kilo base per million mapped readsFormulaRPKM = numReads / ( geneLength/1000 * totalNumReads/1,000,000 )numReads - number of reads mapped to a gene sequencegeneLength - length of the gene sequencetotalNumReads - total number of mapped reads of a sampleCPM - counts per millionFormulaCPM = readsMappedToGene * 1/totalNumReads * 106totalNumReads - total number of mapped reads of a samplereadsMappedToGene - number of reads mapped to a selected geneRead more Note, when applied to gene expression RNA-seq data, RPKM can show a bias for lowly expressed genes. http://bib.oxfordjournals.org/content/early/2012/09/15/bib.bbs046.long#sec-2 TPM (transcripts per million) as alternative to RPKM (in case of comparing identical genes across samples) http://blog.nextgenetics.net/?e=51#body-anchor http://www.ncbi.nlm.nih.gov/pubmed/22872506 |
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