ASpli: An integrative R package for analysing alternative splicing using RNAseq
نویسندگان
چکیده
3 Running ASpli 2 3.1 To BIN or not to BIN . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 3.2 Read Counting . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 3.2.1 Mapping file and bam loading . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3.2.2 Overlap features and read alignments . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 3.3 Alternative splicing analysis and discovery using junction . . . . . . . . . . . . . . . . . . . . . . . . . . 5 3.4 Estimating differential gene expression and bin/junction usage . . . . . . . . . . . . . . . . . . . . . . . 6 3.4.1 Differential gene expression (DE) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 3.4.2 Differential junctions and bin usage (DU) . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 3.5 Output and results . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 7 3.6 Plots . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
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