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TopHat: discovering splice junctions with RNA-Seq
TLDR
The TopHat pipeline is much faster than previous systems, mapping nearly 2.2 million reads per CPU hour, which is sufficient to process an entire RNA-Seq experiment in less than a day on a standard desktop computer. Expand
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation.
TLDR
The results suggest that Cufflinks can illuminate the substantial regulatory flexibility and complexity in even this well-studied model of muscle development and that it can improve transcriptome-based genome annotation. Expand
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks
TLDR
This protocol begins with raw sequencing reads and produces a transcriptome assembly, lists of differentially expressed and regulated genes and transcripts, and publication-quality visualizations of analysis results, which takes less than 1 d of computer time for typical experiments and ∼1 h of hands-on time. Expand
Near-optimal probabilistic RNA-seq quantification
TLDR
Kallisto pseudoaligns reads to a reference, producing a list of transcripts that are compatible with each read while avoiding alignment of individual bases, which removes a major computational bottleneck in RNA-seq analysis. Expand
Differential analysis of gene regulation at transcript resolution with RNA-seq
TLDR
Cuffdiff 2, an algorithm that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries, robustly identifies differentially expressed transcripts and genes and reveals differential splicing and promoter-preference changes. Expand
Initial sequencing and comparative analysis of the mouse genome.
TLDR
The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences. Expand
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
TLDR
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts. Expand
Identification of novel transcripts in annotated genomes using RNA-Seq
TLDR
An algorithm for reference annotation-based transcript assembly is presented and it is shown how it can be used to rapidly investigate novel transcripts revealed by RNA-Seq in comparison with a reference annotation. Expand
Improving RNA-Seq expression estimates by correcting for fragment bias
TLDR
Improvements in expression estimates as measured by correlation with independently performed qRT-PCR are found and correction of bias leads to improved replicability of results across libraries and sequencing technologies. Expand
Streaming fragment assignment for real-time analysis of sequencing experiments
TLDR
eXpress is a software package for efficient probabilistic assignment of ambiguously mapping sequenced fragments that can determine abundances of sequenced molecules in real time and can be applied to ChIP-seq, metagenomics and other large-scale sequencing data. Expand
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