What are Bowtie TopHat and cufflinks?

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 TopHat in RNA-Seq?

TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.

What are bioinformatics cufflinks?

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 TopHat bioinformatics?

TopHat is an open-source bioinformatics tool for the throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo. TopHat aligns RNA-Seq reads to mammalian-sized genomes.

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 DESeq?

DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression. The package is available via Bioconductor and can be conveniently installed as follows: Start an R session and type source(“http://www.bioconductor.org/biocLite.R”) biocLite(“DESeq”)

How do you run TopHat?

Before running Tophat, you have to make an index file that will be used by Tophat. just give any index name (for ex; myindexname). then, in Tophat analysis, for the argument index in Tophat command, just type “myindexname” and run.

What is HT seq?

HTSeq is a Python package that calculates the number of mapped reads to each gene.

What is the difference between a gene and an expressed gene?

Gene expression refers to the process by which the instructions in our DNA are converted into a functional product, such as a protein, while gene regulation refers to the process involved in turning genes on and off to ensure the appropriate expression of genes at the proper times.

What is the difference between a gene and alleles?

A gene is a unit of hereditary information. Except in some viruses, genes are made up of DNA, a complex molecule that codes genetic information for the transmission of inherited traits. Alleles are also genetic sequences, and they too code for the transmission of traits.

What is the difference between DESeq and DESeq2?

The DESeq method is implemented in the R packages DESeq and DESeq2. The latter is more recent, and recommended. The DESeq2 package is also available in several versions, tied to different versions of R (this applies to all Bioconductor packages). Also note that DESeq2 strictly requires R version 3.0 or above.

How does DESeq2 normalize?

DESeq2 performs an internal normalization where geometric mean is calculated for each gene across all samples. The counts for a gene in each sample is then divided by this mean. DESeq2 detects automatically count outliers using Cooks’s distance and removes these genes from analysis.

What is the difference between bowtie and TopHat for read alignment?

Tophat uses Bowtie in the beginning to analyze the reads, but then does more to analyze the reads that span exon-exon junctions. If you are using TopHat for RNA-Seq data, you will get more read aligned against the reference genome.

What is tophat bioinformatics?

TopHat (bioinformatics) TopHat is an open-source bioinformatics tool for the fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies (e.g. RNA-Seq) using Bowtie first and then mapping to a reference genome to discover RNA splice sites de novo.

What is tophat and how do I use it?

TopHat is used to align reads from an RNA-Seq experiment. It is a read-mapping algorithm and it aligns the reads to a reference genome. It is useful because it does not need to rely on known splice sites. TopHat can be used with the Tuxedo pipeline, and is frequently used with Bowtie .

Does Bowtie 2 support colicolorspace (solid) reads?

Colorspace (SOLiD) reads require the older version of Bowtie, since Bowtie 2 does not provide support for this kind of reads.