What is cufflinks used for RNA-Seq?

What is cufflinks used for RNA-Seq?

Cufflinks assembles individual transcripts from RNA-seq reads that have been aligned to the genome. Because a sample may contain reads from multiple splice variants for a given gene, Cufflinks must be able to infer the splicing structure of each gene.

What are bioinformatics cufflinks?

Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.

What is TopHat2?

TopHat is a popular spliced aligner for RNA-sequence (RNA-seq) experiments. TopHat2 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.

What is Hisat?

HISAT (hierarchical indexing for spliced alignment of transcripts) is a highly efficient system for aligning reads from RNA sequencing experiments.

Why did the top hat go out of style?

The top hat fell out of favour in the early 20th century as slowly more casual styles of headwear, such as the bowler hat, became accepted for everyday wear. The art of top hat making is dying out, with only a handful of hatters still plying their trade.

Which is an example of an alternative splicing?

Alternative Splicing. A single gene can contain numerous exons and introns, and the exons can be spliced together in different ways. For example, if a gene contains 10 exons, one version of the mRNA transcribed from that gene might contain exons 1-9. Another version of the mRNA might contain exons 1-8, and exon 10.

How are cufflinks used to study muscle development?

These 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. doi:10.1038/nbt.1621

How are the exons of a gene spliced together?

A single gene can contain numerous exons and introns, and the exons can be spliced together in different ways. For example, if a gene contains 10 exons, one version of the mRNA transcribed from that gene might contain exons 1-9. Another version of the mRNA might contain exons 1-8, and exon 10.

What happens to the mRNA during alternative splicing?

In alternative splicing, interactions between different proteins, the cell, and the environment can cause different segments of the original DNA to be omitted from the mRNA. When this happens, the alternate mRNA is translated into an entirely different protein.

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