What is Cufflinks software?
Cufflinks is a transcript assembly program that includes a number of tools for analyzing RNA-Seq data. These tools assemble aligned RNA-Seq reads into transcripts, estimate their abundances, test for differential expression and regulation, and provide transcript quantification.
What are bowtie TopHat and Cufflinks?
Bowtie33 forms the algorithmic core of TopHat, which aligns millions of RNA-seq reads to the genome per CPU hour. TopHat’s read alignments are assembled by Cufflinks and its associated utility program to produce a transcriptome annotation of the genome.
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 is Cuffdiff?
Cuffdiff estimates the number of fragments that originated from each transcript, primary transcript, and gene in each sample. Primary transcript and gene counts are computed by summing the counts of transcripts in each primary transcript group or gene group.
What is the difference between gene and transcript?
Transcripts are defined as RNA molecules that are made from a DNA template. While most genes are associated with multiple transcripts, each transcript is only assigned to a single gene (at least in databases). In other words, different genes never share the same transcript.
What is the transcriptome of a cell?
A transcriptome is the full range of messenger RNA, or mRNA, molecules expressed by an organism. The term “transcriptome” can also be used to describe the array of mRNA transcripts produced in a particular cell or tissue type.
How many transcripts can a gene have?
Although there are fewer than 22,000 protein coding genes known in the human genome, they are transcribed into over 140,000 different transcripts (Ensembl release 66 ), over 65% of which have protein coding potential and thus may contribute to protein diversity.
Is RNA transcribed?
Transcription is the process by which the information in a strand of DNA is copied into a new molecule of messenger RNA (mRNA). The newly formed mRNA copies of the gene then serve as blueprints for protein synthesis during the process of translation.
What is RNA transcriptome?
What can tophat and cufflinks do for You?
Together, they allow biologists to identify new genes and new splice variants of known ones, as well as compare gene and transcript expression under two or more conditions. This protocol describes in detail how to use TopHat and Cufflinks to perform such analyses.
What is cufflinks used for in RNA sequencing?
Cufflinks. Transcriptome assembly and differential expression analysis for RNA-Seq. Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts.
Do I need a reference genome for tophat or cufflinks?
In particular, TopHat and Cufflinks require a sequenced genome (see below for references to tools that can be used without a reference genome). This protocol also assumes that RNA-seq was performed with either Illumina or SOLiD sequencing machines.
What is the difference between cufflinks 8 and cuffdiff?
Cufflinks 8 ( http://cufflinks.cbcb.umd.edu/) uses this map against the genome to assemble the reads into transcripts. Cuffdiff, a part of the Cufflinks package, takes the aligned reads from two or more conditions and reports genes and transcripts that are differentially expressed using a rigorous statistical analysis.