{"id":28512492,"url":"https://github.com/ncbi/tpmcalculator","last_synced_at":"2025-07-04T01:30:55.106Z","repository":{"id":50465082,"uuid":"124586036","full_name":"ncbi/TPMCalculator","owner":"ncbi","description":"TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files","archived":false,"fork":false,"pushed_at":"2024-06-21T20:45:45.000Z","size":7681,"stargazers_count":130,"open_issues_count":17,"forks_count":33,"subscribers_count":19,"default_branch":"master","last_synced_at":"2025-06-09T00:41:14.034Z","etag":null,"topics":["ngs","rna-seq","tpm"],"latest_commit_sha":null,"homepage":"","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ncbi.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null}},"created_at":"2018-03-09T19:47:15.000Z","updated_at":"2025-04-23T13:41:31.000Z","dependencies_parsed_at":"2022-08-05T15:30:48.067Z","dependency_job_id":"76b0d7e3-f127-4d9e-8066-da10b3a2f6f2","html_url":"https://github.com/ncbi/TPMCalculator","commit_stats":null,"previous_names":[],"tags_count":4,"template":false,"template_full_name":null,"purl":"pkg:github/ncbi/TPMCalculator","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2FTPMCalculator","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2FTPMCalculator/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2FTPMCalculator/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2FTPMCalculator/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ncbi","download_url":"https://codeload.github.com/ncbi/TPMCalculator/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ncbi%2FTPMCalculator/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263430240,"owners_count":23465359,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["ngs","rna-seq","tpm"],"created_at":"2025-06-09T00:38:13.738Z","updated_at":"2025-07-04T01:30:55.091Z","avatar_url":"https://github.com/ncbi.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"TPMCalculator\n=============\n\n[![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/tpmcalculator/README.html) [![Anaconda-Server Badge](https://anaconda.org/bioconda/tpmcalculator/badges/downloads.svg)](https://anaconda.org/bioconda/tpmcalculator) [![Anaconda-Server Badge](https://anaconda.org/bioconda/tpmcalculator/badges/license.svg)](https://anaconda.org/bioconda/tpmcalculator)\n\nTPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files. \nThe input parameters are the same GTF files used to generate the alignments, and one or \nmultiple input BAM file(s) containing either single-end or paired-end sequencing reads. \nThe TPMCalculator output is comprised of four files per sample reporting the TPM values \nand raw read counts for genes, transcripts, exons and introns respectively.\n\n## Reference\n\n * Roberto Vera Alvarez, Lorinc Sandor Pongor, Leonardo Mariño-Ramírez, David Landsman; TPMCalculator: one-step software to quantify mRNA abundance of genomic features, Bioinformatics, , bty896, https://doi.org/10.1093/bioinformatics/bty896\n \n## Conda/Bioconda\n\nTPMCalculator is available on Bioconda: https://bioconda.github.io/recipes/tpmcalculator/README.html\n\n## NIH Biowulf\n\nNIH Biowulf users can load TPMcalculator as a module: https://hpc.nih.gov/apps/TPMCalculator.html    \n\n## Requirements\n\n### BAMTools\n\nClone the BAMTools repository from GitHub: https://github.com/pezmaster31/bamtools\n\nCompile it on this way and set the environment variables for TPMCalculator:\n\n    cd bamtools\n    mkdir build\n    cd build\n    cmake -DCMAKE_INSTALL_PREFIX=../ ..\n    make\n    make install\n    cd ..\n    export BAMTOOLS_DIR=`pwd`\n    export CPPFLAGS=\"-I $BAMTOOLS_DIR/include/bamtools/\"\n    export LDFLAGS=\"-L $BAMTOOLS_DIR/lib64 -Wl,-rpath,$BAMTOOLS_DIR/lib64\"\n\nThat's it. BAMTools was compiled and the env variables were set for compiling\nTPMCalculator.\n\n## Installation\n\nAfter the installation of BAMTools go to the TPMCalculator folder and do make:\n\n    make\n\nA bin folder will be created with the TPMCalculator executable.\n\n## Docker\n\nUse provided [Dockerfile](https://raw.githubusercontent.com/ncbi/TPMCalculator/master/Dockerfile) \nbased on the [BioContainers](https://biocontainers.pro/) base image.\n\n    docker build -t biocontainers/tpmcalculator:0.0.1 https://raw.githubusercontent.com/ncbi/TPMCalculator/master/Dockerfile\n\n    docker run -v /path_to_data:/data --user=yourUID:your:GID biocontainers/tpmcalculator:0.0.1 TPMCalculator -g /data/path_to_GTF/genes.gtf -b /data/path_to_bam/sample1.bam\n\n## [CWL](https://github.com/common-workflow-language)\n\nA CWL tool definition is also provided [tpmcalculator.cwl](https://raw.githubusercontent.com/ncbi/TPMCalculator/master/tpmcalculator.cwl)\n\nUse it like this:\n\n    cwl-runner tpmcalculator.cwl --out_stderr=test.stderr --out_stdout=test.stdout -g genes.gtf -b sample_1.bam\n\n## Usage\n\nUsage: ./bin/TPMCalculator -g GTF_file [-d BAM_files_directory|-b BAM_file] \n\n    ./bin/TPMCalculator options:\n\n        -v    Print info\n        -h    Display this usage information.\n        -g    GTF file\n        -d    Directory with the BAM files\n        -b    BAM file\n        -k    Gene key to use from GTF file. Default: gene_id\n        -t    Transcript key to use from GTF file. Default: transcript_id\n        -c    Smaller size allowed for an intron created for genes. Default: 16. We recommend to use the reads length\n        -p    Use only properly paired reads. Default: No. Recommended for paired-end reads.\n        -q    Minimum MAPQ value to filter out reads. Default: 0. This value depends on the aligner MAPQ value.\n        -o    Minimum overlap between a reads and a feature. Default: 8.\n        -e    Extended output. This will include transcript level TPM values. Default: No.\n        -a    Print out all features with read counts equal to zero. Default: No.\n\n## Description\n\nThe model to describe the genomic features used for a gene is created from the GTF provided \nby the user. TPMCalculator performs two transformations which are executed on the genomic \ncoordinates generating regions for the genes that include the exons and “pure” intron \nregions as shown in Figure S1. The first transformation creates overlapped exons for \nall alternative spliced forms of the genes. A single gene model is generated with unique \nexons and introns which includes the sequence of all exonic regions. The second transformation \nprocess creates a list of pure intron regions that replace those generated by the first \ntransformation. We should indicate that only the intron regions are modified to generate \nregions not overlapped by exons of other genes. Reporting TPM values for these unique \nintrons allows further identification of alternative splicing events like intron retention.\nAdditionally, a set of non-overlapped gene features (exons and introns) are generated and \nused for TPM calculation.\n\n![Gene model](https://github.com/ncbi/TPMCalculator/raw/master/doc/Gene_model.png)\n\n## Validation\n\n* [UCSC hg19](https://github.com/ncbi/TPMCalculator/wiki/Validation#validation-using-ucsc-hg19-genome-annotation)\n* [Gencode v25](https://github.com/ncbi/TPMCalculator/wiki/Validation#validation-using-gencode-v25-genome-annotation)\n\nFor more detailed description and instalation guide lines see https://github.com/ncbi/TPMCalculator/wiki/\n\n## Credits\n\nRoberto Vera Alvarez\nEmail: veraalva@ncbi.nlm.nih.gov\n\nLorinc Pongor\nEmail: pongorlorinc@gmail.com\n\nLeonardo Mariño-Ramírez\nEmail: marino@ncbi.nlm.nih.gov\n\nDavid Landsman\nEmail: landsman@ncbi.nlm.nih.gov\n\n# Public Domain notice\n\n## National Center for Biotechnology Information.\n\nThis software is a \"United States Government Work\" under the terms of the United States\nCopyright Act. It was written as part of the authors' official duties as United States\nGovernment employees and thus cannot be copyrighted. This software is freely available\nto the public for use. The National Library of Medicine and the U.S. Government have not\nplaced any restriction on its use or reproduction.\n\nAlthough all reasonable efforts have been taken to ensure the accuracy and reliability\nof the software and data, the NLM and the U.S. Government do not and cannot warrant the\nperformance or results that may be obtained by using this software or data. The NLM and\nthe U.S. Government disclaim all warranties, express or implied, including warranties\nof performance, merchantability or fitness for any particular purpose.\n\nPlease cite NCBI in any work or product based on this material.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fncbi%2Ftpmcalculator","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fncbi%2Ftpmcalculator","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fncbi%2Ftpmcalculator/lists"}