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TPMCalculator: One-step Software to Quantify MRNA Abundance of Genomic Features

Overview
Journal Bioinformatics
Publisher Oxford University Press
Specialty Biology
Date 2018 Nov 1
PMID 30379987
Citations 98
Authors
Roberto Vera Alvarez
Lorinc Sandor Pongor
Leonardo Marino-Ramirez
David Landsman
Affiliations
Soon will be listed here.
Abstract

Summary: The quantification of RNA sequencing (RNA-seq) abundance using a normalization method that calculates transcripts per million (TPM) is a key step to compare multiple samples from different experiments. TPMCalculator is a one-step software to process RNA-seq alignments in BAM format and reports TPM values, raw read counts and feature lengths for genes, transcripts, exons and introns. The program describes the genomic features through a model generated from the gene transfer format file used during alignments reporting of the TPM values and the raw read counts for each feature. In this paper, we show the correlation for 1256 samples from the TCGA-BRCA project between TPM and FPKM reported by TPMCalculator and RSeQC. We also show the correlation for raw read counts reported by TPMCalculator, HTSeq and featureCounts.

Availability And Implementation: TPMCalculator is freely available at https://github.com/ncbi/TPMCalculator. It is implemented in C++14 and supported on Mac OS X, Linux and MS Windows.

Supplementary Information: Supplementary data are available at Bioinformatics online.

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