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A method and system for quantitative expression of transcriptome data

A transcriptome and data technology, applied in the field of bioinformatics, can solve the problem of high cost and achieve the effect of overcoming limitations

Active Publication Date: 2021-09-24
FUJIAN AGRI & FORESTRY UNIV
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

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Problems solved by technology

The cost of this method is relatively high, and corresponding standard products need to be purchased

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  • A method and system for quantitative expression of transcriptome data
  • A method and system for quantitative expression of transcriptome data
  • A method and system for quantitative expression of transcriptome data

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Embodiment 1

[0025] figure 1 The embodiment of the present invention provides a flow chart of a method for quantitative expression of transcriptome data. Such as figure 1 As shown, the expression quantification methods of the transcriptome data include:

[0026] Step S101: Sequencing the transcriptome sample to obtain data. Compare the data to the reference genome to obtain the comparison result;

[0027] Methods for sequencing transcriptome samples include but are not limited to the Illumina platform, and methods for comparing data to reference genomes include but are not limited to BWA.

[0028] Step S102: processing the comparison results, and counting the sequencing depth of a single base;

[0029] Specifically, the alignment results are processed, and the sequencing depth of a single base is counted by the SAMtools software. The method of counting the sequencing depth of a single base includes but is not limited to the SAMtools software.

[0030] Step S103: Calculate the average ...

Embodiment 2

[0040] image 3 An embodiment of the present invention provides an expression quantification system for transcription data. Such as image 3 As shown, the transcriptional data expression quantification system includes: a sequencing unit 31 , a comparison unit 32 , a processing unit 33 , a calculation unit 34 , a determination unit 35 and a quantification unit 36 ​​.

[0041] The sequencing unit 31 is used to sequence the transcriptome samples to obtain data; the comparison unit 32 is used to compare the data to the reference genome to obtain the comparison results; the processing unit 33 is used to process the comparison results to obtain single-base Sequencing depth; calculation unit 34, used to calculate the average sequencing depth of exons according to the sequencing depth of single bases and the length of exons; determining unit 35, used to perform clustering according to the average sequencing depth of exons, and determine internal reference genes; The quantification u...

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Abstract

The invention discloses a quantitative expression method and system of transcriptome data. The expression quantitative method of transcriptome data includes: sequencing transcriptome samples to obtain data, and comparing the data to a reference genome to obtain comparison results; Process the comparison results to obtain the sequencing depth of single base; calculate the average sequencing depth of exons according to the sequencing depth of single base and the length of exons; perform clustering according to the average sequencing depth of exons to determine the internal reference genes; The average sequencing depth of exons and the average sequencing depth of exons of internal reference genes were used to normalize and quantify the transcriptome data.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a method and system for quantitative expression of transcriptome data. Background technique [0002] At present, the quantitative information analysis methods of transcriptome mainly use the following two methods: [0003] 1. FPKM (Fragments Per Kilobase per Million mapped reads). Represents the number of fragments per kilobase length of a gene in every million sequenced fragments. FPKM is the number of fragments mapped to the gene divided by the number of all fragments mapped to the genome (in millions) and the length of the RNA (in KB). [0004] 2. Relative quantification based on conserved genes. When constructing the RNA library, a certain proportion of standards containing conserved genes is added according to the content of the cells. After the sequencing is completed, the expression level of the gene will be compared with the standard to obtain A relative...

Claims

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Application Information

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Patent Type & Authority Patents(China)
IPC IPC(8): C12Q1/6869G16B30/10G16B40/30
CPCC12Q1/6869G16B25/00
Inventor 何玮毅詹东亮尤民生
Owner FUJIAN AGRI & FORESTRY UNIV