Analysis method for multi-sample-size comparative transcriptomes based on third-generation sequencing detection

A technology of transcriptome analysis and analysis method, which is applied in the field of transcriptome analysis based on three-generation sequencing detection and comparison of multiple samples, and can solve the problems of rare analysis methods

Active Publication Date: 2020-05-15
BIOMARKER TECH
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Problems solved by technology

[0003] As the cost of sequencing decreases year by year, more and more researchers are inclined to sequence analysis with multiple samples, but the analysis method based on comparative transcriptome is still relatively rare

Method used

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  • Analysis method for multi-sample-size comparative transcriptomes based on third-generation sequencing detection
  • Analysis method for multi-sample-size comparative transcriptomes based on third-generation sequencing detection
  • Analysis method for multi-sample-size comparative transcriptomes based on third-generation sequencing detection

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example 1

[0105] Example 1. Based on the three-generation comparative transcriptome analysis method with multiple sample sizes, the macro-evolution analysis of 8 samples is applied, and the macro-evolution analysis of 8 samples includes the following steps:

[0106] a. Pacbio off-machine data quality control, filter joints, and filter reads with fragments less than 300bp. After quality control, the Clean data data of the 8 samples are shown in Table 1 below:

[0107] Table 1

[0108]

[0109] Among them, Samples is the sample name, Reads of Insert is the number of ROI sequences, Mean Read Length of Insert is the quality value of ROI sequences, and Mean Number of Passes is the average sequencing depth (passes) of all ZMW sequences in the cell.

[0110] b. Acquisition of full-length transcripts, according to the software smrtlink7.0, use the ccs program to extract highly consistent consensus sequences from Clean data data, and then use the cluster in Isoseq3 to cluster the consensus s...

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Abstract

An embodiment of the invention provides an analysis method for multi-sample-size comparative transcriptomes based on third-generation sequencing detection. The method comprises the following steps: carrying out quality control on data obtained after third-generation sequencing, acquiring a third-generation full-length transcript, carrying out CDS and PEP prediction, carrying out gene family clustering based on prediction results, and acquiring orthologous genes, paralogous genes and species-specific genes; carrying out macroscopic evolution analysis, SSR detection and marker development on theorthologous genes, carrying out functional gene localization, and excavating tachytelic evolution genes of different subspecies or near-source species of a researched material; carrying out WGD eventdetection and gene family tree analysis of individual families on the paralogous genes; and subjecting the species-specific genes to database annotation to clearly learn about the specific functionsof the specific genes of the researched material. The embodiment of the invention provides a set of perfect scientific research method for bioinformatics research on the whole so as to realize processing of multi-sample-size comparative transcriptome data.

Description

technical field [0001] The invention belongs to the technical field of bioinformatics, and in particular relates to a transcriptome analysis method based on three-generation sequencing detection and comparison of multiple samples. Background technique [0002] With the rapid development of sequencing technology, many genomes have been assembled, and comparative genomics has become an important means to study the evolutionary relationship between these species and closely related species, and to find genes related to the evolution of species. However, compared with species whose genomes have been sequenced, species whose genomes have not been sequenced still account for the vast majority. There are two reasons for this. One is that based on the current sequencing technology, the cost of assembling a genome is still very expensive; the other is that the genomes of some species are relatively complex, such as species with large genomes and polyploid species, which are very diff...

Claims

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Application Information

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IPC IPC(8): G16B20/00
CPCG16B20/00Y02A90/10
Inventor 郑洪坤王运通李绪明
Owner BIOMARKER TECH
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