========================================================================= digitagCT -- Combining DGE and RNA-Sequencing data from CRAC mapping ========================================================================= OVERVIEW: -------- The digitagCT distribution is part of the CracTools. All files are self documented using the POD format and tools. DESCRIPTION: ----------- INSTALLATION: ----------- To install this module type the following: ``` perl Makefile.PL make make test make install ``` USAGE: ----- Once the installation is performed, the sotware binary 'digitagCT' should be available. However, one last step is required before you can use digitagCT software, you need to obtain an annotation file in GFF3 format. To do this, CracTools-core provide a script that is capable of such a thing using Ensembl Perl API, it is called buildGFF3FromEnsembl.pl. You can also provide your own GFF3 file, this format is detailed here: http://www.sequenceontology.org/gff3.shtml. Note that a supplementary attribute 'type' for mRNA features is required in digitagCT. This attribute represent the type of the mRNA, it could be either a 'protein_coding' or any other string. If it is not 'protein_coding' the mRNA will be considered as 'non_coding'. A subtype can be precised using a ':' colon separator (example : protein_coding:pseudogene). INPUT FILE FORMATS: ------------ * `--gff` <FILE>. A GFF3 file format with annotation * `--rna-seq` <FILE>. A SAM file from a mapper (preferably CRAC) * `--sage` <FILE>. A TSV file (Tabulation-Separated Values) with 4 required columns (from transcriRef/SAGE génie DB) * `--tar` <FILE>. A bed file with information about tiling arrays (built from UCSC) More information about the 8 columns of the TSV file: 1. the tag sequence 2. number of occurences of the tag 3. name of the library 4. the total of sequences in the library EXAMPLES: -------- This software is ditributed with some example data files (called 'toys') in folder ./extra/, in order to quickly try the software. Once you have installed the program following instruction provided in section "INSTALLATION" you will be able to launch the software "digitagCT". For more information run `digitagCT --help` or `digitagCT --man` * Generate annotation for DGE tags `digitagCT extra/toyDGE.sam --gff file.gff --summary summary.txt` (Add "ANNOTATION_GFF file.gff" in ~/CracTools.cfg in order to simplify digitagCT command lines.) * Cross DGE tags with RNASeq data `digitagCT extra/toyDGE.sam --rna-seq extra/toyRNASeq.sam` * Cross DGE tags with SAGE genie file `digitagCT extra/toyDGE.sam --sage extra/toySageGenieFile.csv` * Cross DGE tags with tiling arrays `digitagCT extra/toyDGE.sam --tar extra/toyTAR.bed.gz` Note that you can combine the three previous "crossing options" as you want. OUTPUT FILE FORMAT ------------ According to two level of annotation (process A for protein_coding and process B for non_coding), digitag generate a tsv file with the following columns: 1. the tag sequence 2. number of occurences of the tag 3. the annotation process A of the tag 4. the gene name (HUGO Gene Nomenclature Committee) 5. the gene type (protein_coding) 6. Ensembl ID of the Gene 7. chr of the tag sequence 8. location of the tag relative to the chr 9. strand of the tag 10. the annotation process B of the tag 11. the gene name (HUGO Gene Nomenclature Committee) 12. the gene type (non_coding) Other columns about RNA-Seq, TranscriRef and Tiling features are added when the non-mandatory arguments are specified (respectively --rna-seq, --sage, --tar) . DEPENDENCIES: ------------ This package requires these other programs, modules and libraries* : - CracTools-core - perl 5.1 or + - strict - warnings - Carp Notice that almost required modules/libraries are standard. PROBLEMS: -------- COPYRIGHT AND LICENCE: --------------------- Copyright © 2012-2013 -- IRB/INSERM (Institut de Recherches en Biothérapie/ Institut national de la santé et de la recherche médicale). Auteurs/Authors: Jérôme AUDOUX <jerome.audoux@univ-montp2.fr> Alban MANCHERON <alban.mancheron@lirmm.fr> Nicolas PHILIPPE <nicolas.philippe@inserm.fr> ------------------------------------------------------------------------- Ce fichier fait partie de la suite CracTools qui contient plusieurs pipeline intégrés permettant de traiter les évênements biologiques présents dans du RNA-Seq. Les CracTools travaillent à partir d'un fichier SAM de CRAC et d'un fichier d'annotation au format GFF3. Ce logiciel est régi par la licence CeCILL soumise au droit français et respectant les principes de diffusion des logiciels libres. Vous pouvez utiliser, modifier et/ou redistribuer ce programme sous les conditions de la licence CeCILL telle que diffusée par le CEA, le CNRS et l'INRIA sur le site "http://www.cecill.info". En contrepartie de l'accessibilité au code source et des droits de copie, de modification et de redistribution accordés par cette licence, il n'est offert aux utilisateurs qu'une garantie limitée. Pour les mêmes raisons, seule une responsabilité restreinte pèse sur l'auteur du programme, le titulaire des droits patrimoniaux et les concédants successifs. À cet égard l'attention de l'utilisateur est attirée sur les risques associés au chargement, à l'utilisation, à la modification et/ou au développement et à la reproduction du logiciel par l'utilisateur étant donné sa spécificité de logiciel libre, qui peut le rendre complexe à manipuler et qui le réserve donc à des développeurs et des professionnels avertis possédant des connaissances informatiques approfondies. Les utilisateurs sont donc invités à charger et tester l'adéquation du logiciel à leurs besoins dans des conditions permettant d'assurer la sécurité de leurs systêmes et ou de leurs données et, plus généralement, à l'utiliser et l'exploiter dans les mêmes conditions de sécurité. Le fait que vous puissiez accéder à cet en-tête signifie que vous avez pris connaissance de la licence CeCILL, et que vous en avez accepté les termes. ------------------------------------------------------------------------- This file is part of the CracTools which provide several integrated pipeline to analyze biological events present in RNA-Seq data. CracTools work on a SAM file generated by CRAC and an annotation file in GFF3 format. This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL "http://www.cecill.info". As a counterpart to the access to the source code and rights to copy, modify and redistribute granted by the license, users are provided only with a limited warranty and the software's author, the holder of the economic rights, and the successive licensors have only limited liability. In this respect, the user's attention is drawn to the risks associated with loading, using, modifying and/or developing or reproducing the software by the user in light of its specific status of free software, that may mean that it is complicated to manipulate, and that also therefore means that it is reserved for developers and experienced professionals having in-depth computer knowledge. Users are therefore encouraged to load and test the software's suitability as regards their requirements in conditions enabling the security of their systems and/or data to be ensured and, more generally, to use and operate it in the same conditions as regards security. The fact that you are presently reading this means that you have had knowledge of the CeCILL license and that you accept its terms.