Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation¶

Why this mattered¶

TBD

(no abstract available)

cite → The Sequence Alignment/Map format and SAMtools — Cufflinks uses SAM/BAM alignment files and SAMtools conventions as the input representation for RNA-Seq transcript assembly and quantification.
cite → Ultrafast and memory-efficient alignment of short DNA sequences to the human genome — Cufflinks uses Bowtie's ultrafast short-read alignments as upstream evidence for reconstructing transcripts from RNA-Seq reads.
cite → Mapping and quantifying mammalian transcriptomes by RNA-Seq — Cufflinks extends RNA-Seq transcriptome mapping and quantification from gene-level expression toward transcript assembly, novel isoforms, and isoform switching.
enables → Tissue-based map of the human proteome — RNA-Seq transcript quantification and isoform discovery provided tissue expression evidence that the Human Proteome Map used to connect proteins to transcripts.
cite ← Circular RNAs are a large class of animal RNAs with regulatory potency — The circular-RNA study used Cufflinks-style transcript assembly and RNA-seq quantification concepts to compare circular and linear transcript expression.
cite ← Tissue-based map of the human proteome — The human proteome map uses RNA-seq transcript quantification methods such as Cufflinks-style assembly to compare protein expression with transcript abundance.