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All splice samples in library1/17/2024 ![]() This information is obtained once initially, and can then be used for all future analyses. When starting a new project, SGSeq requires information about the samples to be analyzed. ![]() \(^\ast\) SGVariantCounts assay countsVariant5pOr3p can only be obtained from BAM files, for details see section Testing for differential splice variant usage. SGFeatureCounts and SGVariantCounts extend SummarizedExperiment and are containers for per-sample counts (or other expression values) along with corresponding SGFeatures and SGVariants objects. ![]() 2013): TxFeatures and SGFeatures extend GRanges, SGVariants extends CompressedGRangesList. SGSeq makes extensive use of Bioconductor infrastructure for genomic ranges (Lawrence et al. Dashed arrows indicate functions analyzeFeatures() and analyzeVariants(), which wrap multiple analysis steps. Classes are shown in bold and outlined, function names are shown in italics. ( b) SGSeq representation of concepts shown in (a). Splice events are defined in an augmented graph with a unique source and sink node for each gene, connected to alternative starts and ends, respectively (dashed lines). ( a) Schematic illustrating transcripts, discrete transcript features, the splice graph, and splice events consisting of alternative splice variants. Goldstein LD, Cao Y, Pau G, Lawrence M, Wu TD, Seshagiri S, Gentleman R (2016) Prediction and Quantification of Splice Events from RNA-Seq Data.Splice variants sharing the same start and end node, together form a splice event. If two nodes in the splice graph are connected by two or more paths, and there are no intervening nodes with all paths intersecting, the alternative paths are considered splice variants. The SGVariants class stores splice variants.It is directed from the 5 \(^\prime\) end to the 3 \(^\prime\) end of a gene. The splice graph is a directed acyclic graph with edges corresponding to exonic regions and splice junctions, and nodes corresponding to transcript starts, ends and splice sites. The SGFeatures class stores features defining a splice graph (Heber et al.These can be extracted from annotation or predicted from aligned RNA-seq reads. The TxFeatures class stores discrete transcript features (exons and splice junctions) as they are observed in RNA transcripts.An overview of SGSeq classes and how they are related is shown in Figure 1 and summarized below: SGSeq provides functions and data structures for analyzing splice events from RNA-seq data.
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