{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,30]],"date-time":"2026-03-30T20:36:41Z","timestamp":1774903001489,"version":"3.50.1"},"reference-count":9,"publisher":"Oxford University Press (OUP)","issue":"11","funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"name":"National Library of Medicine and National Center for Biotechnology Information"},{"DOI":"10.13039\/100000092","name":"National Library of Medicine","doi-asserted-by":"publisher","award":["UNKP-17-3"],"award-info":[{"award-number":["UNKP-17-3"]}],"id":[{"id":"10.13039\/100000092","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,6,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Summary<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Availability and implementation<\/jats:title>\n                  <jats:p>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.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Supplementary information<\/jats:title>\n                  <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/bioinformatics\/bty896","type":"journal-article","created":{"date-parts":[[2018,10,30]],"date-time":"2018-10-30T20:15:11Z","timestamp":1540930511000},"page":"1960-1962","source":"Crossref","is-referenced-by-count":244,"title":["TPMCalculator: one-step software to quantify mRNA abundance of genomic features"],"prefix":"10.1093","volume":"35","author":[{"given":"Roberto","family":"Vera Alvarez","sequence":"first","affiliation":[{"name":"Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA"}]},{"given":"Lorinc Sandor","family":"Pongor","sequence":"additional","affiliation":[{"name":"Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA"},{"name":"2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary"}]},{"given":"Leonardo","family":"Mari\u00f1o-Ram\u00edrez","sequence":"additional","affiliation":[{"name":"Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA"}]},{"given":"David","family":"Landsman","sequence":"additional","affiliation":[{"name":"Computational Biology Branch, National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA"}]}],"member":"286","published-online":{"date-parts":[[2018,10,31]]},"reference":[{"key":"2023012713232398900_bty896-B1","doi-asserted-by":"crossref","first-page":"166","DOI":"10.1093\/bioinformatics\/btu638","article-title":"HTSeq\u2013a Python framework to work with high-throughput sequencing data","volume":"31","author":"Anders","year":"2015","journal-title":"Bioinformatics"},{"key":"2023012713232398900_bty896-B2","doi-asserted-by":"crossref","first-page":"D8","DOI":"10.1093\/nar\/gkx1095","article-title":"Database resources of the National Center for Biotechnology Information","volume":"46","author":"Coordinators","year":"2018","journal-title":"Nucleic Acids Res."},{"key":"2023012713232398900_bty896-B3","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1038\/nature11412","article-title":"Comprehensive molecular portraits of human breast tumours","volume":"490","author":"Koboldt","year":"2012","journal-title":"Nature"},{"key":"2023012713232398900_bty896-B4","doi-asserted-by":"crossref","first-page":"923","DOI":"10.1093\/bioinformatics\/btt656","article-title":"featureCounts: an efficient general purpose program for assigning sequence reads to genomic features","volume":"30","author":"Liao","year":"2014","journal-title":"Bioinformatics"},{"key":"2023012713232398900_bty896-B5","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. 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