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Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
TLDR
Bowtie extends previous Burrows-Wheeler techniques with a novel quality-aware backtracking algorithm that permits mismatches and can be used simultaneously to achieve even greater alignment speeds. Expand
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
TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
TLDR
TopHat2 is described, which incorporates many significant enhancements to TopHat, and combines the ability to identify novel splice sites with direct mapping to known transcripts, producing sensitive and accurate alignments, even for highly repetitive genomes or in the presence of pseudogenes. 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
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
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses.
TLDR
It is found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that l incRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes. Expand
The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells
TLDR
Monocle is described, an unsupervised algorithm that increases the temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points that revealed switch-like changes in expression of key regulatory factors, sequential waves of gene regulation, and expression of regulators that were not known to act in differentiation. 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
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