TPMCalculator: one-step software to quantify mRNA abundance of genomic features

被引：170

作者：

Alvarez, Roberto Vera ^{[1
]}

Pongor, Lorinc Sandor ^{[1
,2
]}

Marino-Ramirez, Leonardo ^{[1
]}

Landsman, David ^{[1
]}

机构：

[1] Natl Ctr Biotechnol Informat, Computat Biol Branch, Natl Lib Med, NIH, Bethesda, MD 20892 USA

[2] Semmelweis Univ, Dept Pediat 2, H-1094 Budapest, Hungary

来源：

BIOINFORMATICS | 2019年 / 35卷 / 11期

基金：

美国国家卫生研究院;

关键词：

QUANTIFICATION;

D O I：

10.1093/bioinformatics/bty896

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

A 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.

引用

页码：1960 / 1962

页数：3

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