P. Bertone, V. Stolc, T. Royce, J. Rozowsky, A. Urban et al., Global Identification of Human Transcribed Sequences with Genome Tiling Arrays, Science, vol.306, issue.5705, pp.2242-2246, 2004.
DOI : 10.1126/science.1103388

J. Kim, G. Porreca, L. Song, S. Greenway, J. Gorham et al., Polony Multiplex Analysis of Gene Expression (PMAGE) in Mouse Hypertrophic Cardiomyopathy, Science, vol.316, issue.5830, pp.1481-1484, 2007.
DOI : 10.1126/science.1137325

E. Rivals, A. Boureux, M. Lejeune, F. Ottones, O. Perez et al., Transcriptome annotation using tandem SAGE tags, Nucleic Acids Research, vol.35, issue.17, p.108, 2007.
DOI : 10.1093/nar/gkm495

URL : https://hal.archives-ouvertes.fr/lirmm-00203923

A. Barski, S. Cuddapah, K. Cui, T. Y. Roh, D. E. Schones et al., High-Resolution Profiling of Histone Methylations in the Human Genome, Cell, vol.129, issue.4, pp.823-837, 2007.
DOI : 10.1016/j.cell.2007.05.009

A. P. Boyle, S. Davis, H. P. Shulha, P. Meltzer, E. H. Margulies et al., High-Resolution Mapping and??Characterization of Open Chromatin across the Genome, Cell, vol.132, issue.2, pp.311-322, 2008.
DOI : 10.1016/j.cell.2007.12.014

S. Saha, A. Sparks, C. Rago, V. Akmaev, C. Wang et al., Using the transcriptome to annotate the genome, Nature Biotechnology, vol.20, issue.5, pp.508-512, 2002.
DOI : 10.1038/nbt0502-508

C. Keime, M. Semon, D. Mouchiroud, L. Duret, and O. Gandrillon, Unexpected observations after mapping LongSAGE tags to the human genome, BMC Bioinformatics, vol.8, issue.1, p.154, 2007.
DOI : 10.1186/1471-2105-8-154

URL : https://hal.archives-ouvertes.fr/hal-00193777

P. Kapranov, J. Cheng, S. Dike, D. Nix, R. Duttagupta et al., RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription, Science, vol.316, issue.5830, pp.1484-1488, 2007.
DOI : 10.1126/science.1138341

G. Robertson, M. Hirst, M. Bainbridge, M. Bilenky, Y. Zhao et al., Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing, Nature Methods, vol.128, issue.8, pp.651-657, 2007.
DOI : 10.1038/nmeth1068

D. S. Johnson, A. Mortazavi, R. Myers, and B. Wold, Genome-Wide Mapping of in Vivo Protein-DNA Interactions, Science, vol.316, issue.5830, pp.316-149, 2007.
DOI : 10.1126/science.1141319

H. Kawaji, T. Kasukawa, S. Fukuda, S. Katayama, C. Kai et al., CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis, Nucleic Acids Research, vol.34, issue.90001, pp.632-636, 2006.
DOI : 10.1093/nar/gkj034

E. Rivals, L. Salmela, P. Kalsi, P. Kiiskinen, and J. Tarhio, mpscan: Fast Localisation of Multiple Reads in Genomes, genomes 9th Workshop on Algorithms in Bioinformatics (WABI'09), 2009.
DOI : 10.1016/j.jcss.2007.10.001

URL : https://hal.archives-ouvertes.fr/lirmm-00407173

S. Robin, F. Rodolphe, and S. Schbath, DNA, Words and Models, pp.57-118, 2005.

E. Rivals and S. Rahmann, Combinatorics of periods in strings, Journal of Combinatorial Theory, Series A, vol.104, issue.1, pp.95-113, 2003.
DOI : 10.1016/S0097-3165(03)00123-7

URL : https://hal.archives-ouvertes.fr/lirmm-00193520

B. Efron and G. Gong, A leisurely look at the bootstrap, the Jackknife, and cross-validation, Am. Stat, vol.37, pp.36-48, 1983.

D. Piquemal, T. Commes, L. Manchon, M. Lejeune, C. Ferraz et al., Transcriptome Analysis of Monocytic Leukemia Cell Differentiation, Genomics, vol.80, issue.3, pp.361-371, 2002.
DOI : 10.1006/geno.2002.6836

J. Colinge and G. Feger, Detecting the impact of sequencing errors on SAGE data, Bioinformatics, vol.17, issue.9, pp.840-842, 2001.
DOI : 10.1093/bioinformatics/17.9.840

M. Harbers and P. Carninci, Tag-based approaches for transcriptome research and genome annotation, Nature Methods, vol.5, issue.7, pp.495-502, 2005.
DOI : 10.1016/0378-1119(94)90802-8

J. M. Johnson, S. Edwards, D. Shoemaker, and E. E. Schadt, Dark matter in the genome: evidence of widespread transcription detected by microarray tiling experiments, Trends in Genetics, vol.21, issue.2, pp.93-102, 2005.
DOI : 10.1016/j.tig.2004.12.009

V. E. Velculescu and K. W. Kinzier, Gene expression analysis goes digital, Nature Biotechnology, vol.316, issue.8, pp.878-880, 2007.
DOI : 10.1038/nbt0807-878

E. R. Mardis, ChIP-seq: welcome to the new frontier, Nature Methods, vol.129, issue.8, pp.613-614, 2007.
DOI : 10.1038/nmeth0807-613

J. C. Dohm, C. Lottaz, T. Borodina, and H. Himmelbauer, Substantial biases in ultra-short read data sets from high-throughput DNA sequencing, Nucleic Acids Research, vol.36, issue.16, p.105, 2008.
DOI : 10.1093/nar/gkn425

J. Khattra, A. D. Delaney, Y. Zhao, A. Siddiqui, J. Asano et al., Large-scale production of SAGE libraries from microdissected tissues, flow-sorted cells, and cell lines, Genome Research, vol.17, issue.1, pp.108-116, 2007.
DOI : 10.1101/gr.5488207

P. Kharchenko, M. Tolstorukov, and P. Park, Design and analysis of ChIP-seq experiments for DNA-binding proteins, Nature Biotechnology, vol.26, issue.12, pp.1351-1359, 2008.
DOI : 10.1016/S0167-9473(99)00100-0

V. R. Akmaev and C. J. Wang, Correction of sequence-based artifacts in serial analysis of gene expression, Bioinformatics, vol.20, issue.8, pp.1254-1263, 2004.
DOI : 10.1093/bioinformatics/bth077

A. Silva, J. D. Souza, P. Galante, G. Riggins, S. D. Souza et al., The impact of SNPs on the interpretation of SAGE and MPSS experimental data, Nucleic Acids Research, vol.32, issue.20, pp.6104-6110, 2004.
DOI : 10.1093/nar/gkh937

R. Redon, S. Ishikawa, K. R. Fitch, L. Feuk, G. H. Perry et al., Global variation in copy number in the human genome, Nature, vol.38, issue.7118, pp.444-454, 2006.
DOI : 10.1126/science.1117196

X. Li, L. Zhao, H. Jiang, and W. Wang, Short Homologous Sequences Are Strongly Associated with the Generation of Chimeric RNAs in Eukaryotes, Journal of Molecular Evolution, vol.27, issue.1, pp.56-65, 2009.
DOI : 10.1007/s00239-008-9187-0

G. Faulkner, A. Forrest, A. Chalk, K. Schroder, Y. Hayashizaki et al., A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE, Genomics, vol.91, issue.3, pp.281-288, 2008.
DOI : 10.1016/j.ygeno.2007.11.003

M. Sultan, M. H. Schulz, H. Richard, A. Magen, A. Klingenhoff et al., A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome, Science, vol.321, issue.5891, pp.956-960, 2008.
DOI : 10.1126/science.1160342