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How to assemble number transcript

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all right um so a little were continuing with you know how we can analyze rna secretes so generally there are kind of two pathways we can choose to go down and its kind of dependent on if theres a reference or not so if there is a reference for example we know all the cvss that exist in a species right theres a reference on ensemble theres a reference on ncbi um well i mean what we would do is just clean our reads up and then map them back to the reference and start counting well eventually do that but if we dont have a reference which is probably is still a little bit more common in comparative genomics than what we have to do as a symbol assemble those reads and so its a little bit the idea is is reasonably simple and its basically to just find overlapping reads that share sequence similarity and more or less build a context from that right just a contiguous sequence of reads that overlap with one another and produce what would be a transcript um and so the whole point is

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What is a transcripts in sequencing?

Transcription is the first step in gene expression. It involves copying a genes DNA sequence to make an RNA molecule. Transcription is performed by enzymes called RNA polymerases, which link nucleotides to form an RNA strand (using a DNA strand as a template).

What software is used for transcriptome assembly?

TRINITY is a software package for conducting de novo (as well as the genome-guided version of) transcriptome assembly from RNA-seq data. The Trinity package also includes a number of perl scripts for generating statistics to assess assembly quality, and for wrapping external tools for conducting downstream analyses.

How do you assess transcriptome assembly?

Transcriptome Assembly Quality Assessment Examine the RNA-Seq read representation of the assembly. Examine the representation of full-length reconstructed protein-coding genes, by searching the assembled transcripts against a database of known protein sequences.

What is meant by transcriptome sequencing?

The set of genes which are transcribed in any one condition is known as the transcriptome, and the process of determining the genetic codes contained in the transcriptome, and their relative proportions, is known as transcriptome sequencing.

How does transcriptome assembly work?

It is a research tool often employed in functional genomics research on non-model species. It works by blasting assembled contigs against a non-redundant protein database (at NCBI), then annotating them based on sequence similarity.

What is meant by transcript assembly?

Transcriptome assembly is a process of reconstructing the complete set of full-length transcripts from RNA-seq data, which often include tens of millions of short-read sequences.

What is de novo assembly without reference?

De novo sequence assemblers are a type of program that assembles short nucleotide sequences into longer ones without the use of a reference genome. These are most commonly used in bioinformatic studies to assemble genomes or transcriptomes.

What is transcript assembly?

Transcriptome assembly is a process of reconstructing the complete set of full-length transcripts from RNA-seq data, which often include tens of millions of short-read sequences.

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