Q. Pan, O. Shai, L. J. Lee, B. J. Frey, and B. J. Blencowe, Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing, Nat Genet, vol.40, pp.1413-1415, 2008.

E. T. Wang, Alternative isoform regulation in human tissue transcriptomes, Nature, vol.456, pp.470-476, 2008.
DOI : 10.1038/nature07509

URL : http://europepmc.org/articles/pmc2593745?pdf=render

M. M. Scotti and M. S. Swanson, Rna mis-splicing in disease, Nature Reviews Genetics, vol.17, pp.19-32, 2016.
DOI : 10.1038/nrg.2015.3

P. Edery, Association of tals developmental disorder with defect in minor splicing component u4atac snrna, Science, vol.332, pp.240-243, 2011.
DOI : 10.1126/science.1202205

URL : https://hal.archives-ouvertes.fr/hal-01017145

C. J. David and J. L. Manley, Alternative pre-mrna splicing regulation in cancer: pathways and programs unhinged, Genes & development, vol.24, pp.2343-2364, 2010.
DOI : 10.1101/gad.1973010

URL : http://genesdev.cshlp.org/content/24/21/2343.full.pdf

C. Trapnell, Differential gene and transcript expression analysis of rna-seq experiments with tophat and cufflinks, Nature protocols, vol.7, pp.562-578, 2012.
DOI : 10.1038/nprot.2012.016

URL : https://authors.library.caltech.edu/74752/3/nihms-366741.pdf

K. Wang, Mapsplice: accurate mapping of rna-seq reads for splice junction discovery, Nucleic acids research, vol.38, pp.178-178, 2010.
DOI : 10.1093/nar/gkq622

URL : https://academic.oup.com/nar/article-pdf/38/18/e178/18784925/gkq622.pdf

G. Robertson, De novo assembly and analysis of rna-seq data, Nature methods, vol.7, pp.909-912, 2010.
DOI : 10.1038/nmeth.1517

T. Steijger, Assessment of transcript reconstruction methods for rna-seq, Nature methods, vol.10, pp.1177-1184, 2013.
DOI : 10.1038/nmeth.2714

URL : https://hal.archives-ouvertes.fr/hal-00909081

S. Anders, A. Reyes, and W. Huber, Detecting differential usage of exons from RNA-seq data, Genome research, vol.22, pp.2008-2025, 2012.
DOI : 10.1038/npre.2012.6837.2

URL : http://precedings.nature.com/documents/6837/version/2/files/npre20126837-2.pdf

Y. Katz, E. T. Wang, E. M. Airoldi, and C. B. Burge, Analysis and design of rna sequencing experiments for identifying isoform regulation, Nature methods, vol.7, pp.1009-1015, 2010.
DOI : 10.1038/nmeth.1528

URL : http://dspace.mit.edu/bitstream/1721.1/83628/1/Burge_Analysis%20and%20design.pdf

S. Shen, MATS: a Bayesian framework for flexible detection of differential alternative splicing from RNA-Seq data, Nucleic Acids Research, pp.61-61, 2012.

G. A. Sacomoto, KISSPLICE: de-novo calling alternative splicing events from RNA-seq data, BMC bioinformatics, vol.13, issue.6, p.5, 2012.
URL : https://hal.archives-ouvertes.fr/hal-00784407

J. A. Martin and Z. Wang, Next-generation transcriptome assembly, Nature Reviews Genetics, vol.12, pp.671-682, 2011.
DOI : 10.1038/nrg3068

URL : https://digital.library.unt.edu/ark:/67531/metadc830328/m2/1/high_res_d/1076789.pdf

D. Dargahi, A pan-cancer analysis of alternative splicing events reveals novel tumor-associated splice variants of matriptase, Cancer informatics, vol.13, p.167, 2014.

F. Freyermuth, Splicing misregulation of scn5a contributes to cardiac-conduction delay and heart arrhythmia in myotonic dystrophy, Nature communications, vol.7, 2016.
URL : https://hal.archives-ouvertes.fr/hal-01301863

M. G. Grabherr, Trinity: reconstructing a full-length transcriptome without a genome from rna-seq data, Nature biotechnology, vol.29, p.644, 2011.
DOI : 10.1038/nbt.1883

URL : http://europepmc.org/articles/pmc3571712?pdf=render

N. M. Kopelman, D. Lancet, and I. Yanai, Alternative splicing and gene duplication are inversely correlated evolutionary mechanisms, Nat Genet, vol.37, pp.588-589, 2005.
DOI : 10.1038/ng1575

J. Roux and M. Robinson-rechavi, Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication, Genome research, vol.21, pp.357-363, 2011.
DOI : 10.1101/gr.113803.110

URL : http://genome.cshlp.org/content/21/3/357.full.pdf

M. A. Batzer and P. L. Deininger, Alu repeats and human genomic diversity, Nature Reviews Genetics, vol.3, pp.370-379, 2002.
DOI : 10.1038/nrg798

G. Lev-maor, R. Sorek, N. Shomron, and G. Ast, The birth of an alternatively spliced exon: 3'splice-site selection in alu exons, Science, vol.300, pp.1288-1291, 2003.

R. Sorek, Minimal conditions for exonization of intronic sequences: 5? splice site formation in alu exons, Molecular cell, vol.14, pp.221-231, 2004.

M. Franz, js: a graph theory library for visualisation and analysis, Bioinformatics, vol.32, pp.309-311, 2016.
DOI : 10.1093/bioinformatics/btv557

URL : https://academic.oup.com/bioinformatics/article-pdf/32/2/309/6689178/btv557.pdf

H. Lopez-maestre, SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence, Nucleic Acids Research, vol.44, pp.148-148, 2016.
DOI : 10.1093/nar/gkw655

URL : https://hal.archives-ouvertes.fr/hal-01352586

, Scientific REPoRTS |, vol.8, p.4307, 2018.

E. M. Poursani, B. M. Soltani, and S. J. Mowla, Differential expression of oct4 pseudogenes in pluripotent and tumor cell lines, Cell Journal (Yakhteh), vol.18, p.28, 2016.

R. Bacher and C. Kendziorski, Design and computational analysis of single-cell rna-sequencing experiments, Genome biology, vol.17, p.1, 2016.

S. Shen, Widespread establishment and regulatory impact of alu exons in human genes, Proceedings of the National Academy of Sciences, vol.108, pp.2837-2842, 2011.

H. Tilgner, F. Grubert, D. Sharon, and M. P. Snyder, Defining a personal, allele-specific, and single-molecule long-read transcriptome, Proceedings of the National Academy of Sciences of the United States of America, vol.111, pp.9869-74, 2014.
DOI : 10.1073/pnas.1400447111

URL : http://www.pnas.org/content/111/27/9869.full.pdf

M. T. Bolisetty, G. Rajadinakaran, and B. R. Graveley, Determining exon connectivity in complex mRNAs by nanopore sequencing, Genome biology, vol.16, p.204, 2015.

P. Mallinjoud, Endothelial, epithelial, and fibroblast cells exhibit specific splicing programs independently of their tissue of origin, Genome research, vol.24, pp.511-521, 2014.
URL : https://hal.archives-ouvertes.fr/hal-01091290

D. Laustriat, In Vitro and In Vivo Modulation of Alternative Splicing by the Biguanide Metformin, Molecular Therapy. Nucleic Acids, vol.4, p.262, 2015.
URL : https://hal.archives-ouvertes.fr/hal-01277500

M. H. Schulz, D. R. Zerbino, M. Vingron, and E. Birney, Oases: robust de novo rna-seq assembly across the dynamic range of expression levels, Bioinformatics, vol.28, pp.1086-1092, 2012.

H. Li, The sequence alignment/map format and samtools, Bioinformatics, vol.25, pp.2078-2079, 2009.

Y. Benjamini and Y. Hochberg, Controlling the false discovery rate: a practical and powerful approach to multiple testing, Journal of the royal statistical society. Series B (Methodological), pp.289-300, 1995.

S. Djebali, Landscape of transcription in human cells, Nature, vol.489, pp.101-108, 2012.
URL : https://hal.archives-ouvertes.fr/hal-01216755

E. Dardenne, RNA Helicases DDX5 and DDX17 Dynamically Orchestrate Transcription, miRNA, and Splicing Programs in Cell Differentiation, Cell Reports, 2014.

R. Schmieder and R. Edwards, Quality control and preprocessing of metagenomic datasets, Bioinformatics, vol.27, pp.863-864, 2011.

M. Martin, Cutadapt removes adapter sequences from high-throughput sequencing reads, EMBnet. journal, vol.17, 2011.

, This work was funded by the ANR12-BS02-0008 (Colib'read) by the ABS4NGS ANR project, Acknowledgements This work was performed on the computing facilities of the computing center LBBE/PRABI and the PSMN, pp.2014-154, 2009.