TPMCalculator

TPMCalculator quantifies mRNA abundance across genomic features using the transcripts per million (TPM) normalization method to provide standardized TPM values, raw read counts, and feature lengths for genes, transcripts, exons, and introns to enable comparison of RNA-seq data across samples and experiments.

Key Features:

• Normalization Methodology: Calculates transcripts per million (TPM) to normalize RNA-seq measurements across samples.
• Input Formats and Feature Model: Processes RNA-seq alignments in BAM format and uses a feature model derived from gene transfer format (GTF) files to define genes, transcripts, exons, and introns.
• Outputs: Generates reports containing TPM values, raw read counts, and feature lengths for genes, transcripts, exons, and introns.
• Validation and Benchmarking: Validated by correlation analysis of 1256 TCGA-BRCA samples comparing TPM to FPKM from RSeQC and showing consistent raw read counts versus HTSeq and featureCounts.
• Implementation: Implemented in C++14.

Scientific Applications:

• Comparative Genomics: Enables comparison of gene expression levels across conditions, tissues, or time points using standardized TPM values.
• Transcriptome Analysis: Supports transcriptome-level analyses by reporting abundance for transcripts, exons, and introns to inform studies of gene regulation and function.

Methodology:

Calculates TPM from RNA-seq BAM alignments using a GTF-derived feature model to report TPM values, raw read counts, and feature lengths; validation performed by correlation analysis against FPKM from RSeQC and read counts from HTSeq and featureCounts on TCGA-BRCA samples.