RNA-Seq De novo Assembly Using Trinity
...length splicing isoforms and to tease apart transcripts derived from paralogous genes...e RNA-seq data into the unique sequences of transcripts, often generating full-length...the graph, ultimately reporting full-length transcripts for alternatively spliced iso...2958 days ago
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Reference-free prediction of rearrangement breakpoint reads
...rectly with no false-positive reads. Moreover, evaluation on a real prostate cancer dataset shows that the proposed method predicts more fusion transcripts correctly than previous appro...2243 days ago
SCUBAT: Scaffolding Contigs Using Blat And Transcripts
SCUBAT (Scaffolding Contigs Using BLAT And Transcripts) uses any set of transcripts to identify cases where a transcript is split over multiple genome fragments and attempts to use this information to scaffold the genome.2238 days ago
G-compass: a comparative genome browser
...c regions between human and other 12 vertebrates based on original genome alignments pursuing higher coverage (1,2). Annotations of human genes/transcripts and their ortholog informatio...2207 days ago
Scallop: reference-based transcriptome assembler for RNA-seq
...callop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts. Scallop achieves this improv...from reads and paired-end reads, while also achieves both transcripts parsimony and coverage deviat...2182 days ago
RNA-seq Analysis Workshop Course Materials
...ference genome and significantly improves our ability to reconstruct transcripts. This category would obviousl...is available. In this case one would need to assemble the reads into transcripts using de novo approaches. Thi...2126 days ago
Ensembl Variation - Calculated variant consequences
...mapped to the reference genome, we identify all overlapping Ensembl transcripts. We then use a rule-based app...each allele of each variant may have a different effect in different transcripts....2057 days ago