Supplementary Methods for the Paper Transcript Assembly and Quantification by Rna-seq Reveals Unannotated Transcripts and Isoform Switching during Cell Differentiation
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چکیده
List of Figures ii List of Tables ii 1. Sequencing experiment 1 2. Mapping fragments to the genome 1 2.1. Discovering splice junctions 2 2.2. Resolving multiple alignments for fragments 2 3. Transcript abundance estimation 4 3.1. Definitions 4 3.2. A statistical model for RNA-Seq 4 3.3. Estimation of parameters 8 3.4. Assessment of abundance estimation 12 4. Transcript assembly 15 4.1. Overview 15 4.2. A partial order on fragment alignments 16 4.3. Assembling a parsimonious set of transcripts 17 4.4. Assessment of assembly quality 19 5. Analysis of gene expression dynamics 24 5.1. Selection of high-confidence transcripts for expression tracking 24 5.2. Testing for changes in absolute expression 25 5.3. Quantifying transcriptional and post-transcriptional overloading 26 6. The Cufflinks software 31 7. Appendix A: Lemmas and Theorems 32 8. Appendix B: selected Minard plots 35 References 39
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تاریخ انتشار 2010