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Automated analysis method for prokaryotic transcriptome based on second generation sequencing

An automated analysis and next-generation sequencing technology, applied in the field of high-throughput sequencing, can solve problems such as unsatisfactory standardized results, waste of labor and time, and inaccurate differential analysis results

Pending Publication Date: 2019-07-23
南京派森诺基因科技有限公司
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Problems solved by technology

[0004] (1) The results are not good: At present, when Rockhopper, an automated prokaryotic transcriptome analysis tool, performs differential analysis on samples, the standardized results are not satisfactory, resulting in inaccurate differential analysis results.
[0005] (2) There is no other automated analysis platform: the analysis process for each step of the prokaryotic transcriptome is relatively fixed, but the results need to be sorted out manually and the work of each step is connected, which is a waste of labor and time

Method used

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  • Automated analysis method for prokaryotic transcriptome based on second generation sequencing
  • Automated analysis method for prokaryotic transcriptome based on second generation sequencing
  • Automated analysis method for prokaryotic transcriptome based on second generation sequencing

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Embodiment Construction

[0030] The present invention will be further described by the following examples, but these examples should not be used to explain the limitation of the present invention.

[0031] see process figure 1 , the steps of the present invention include:

[0032] S1) Prepare and read the config file, which includes: off-machine data location and corresponding sample name and group name, grouping for differential analysis, path for saving analysis results, task name, genome sequence and its index file location, GTF files and other information. When the software reads the relevant information, it will generate shell scripts corresponding to all the analysis steps listed below, and run them in order. There will be a running log for each step while running, which is convenient for result checking. All analytical steps are briefly described below.

[0033] The first is raw off-board data filtering. As an example, use the perl script independently developed by Pysennuo to filter the or...

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Abstract

The invention discloses an automated analysis method for prokaryotic transcriptome based on second generation sequencing. The automated analysis method includes the steps: an original logout data filtering and quality control step; a genome comparison step; a transcript structure analysis step; a gene expression quantification and differential expression analysis step; and a result sorting step. The automated analysis method for prokaryotic transcriptome based on second generation sequencing has the advantages of: covering most of the analysis content required by the market, automatically sorting out all the analysis results, and after completing the analysis of each part, automatically counting, visualizing, and sorting the results, so that the results are arranged in order and can be directly used for generation of a report; being visible for all the operation steps, thus being convenient for error query; and when performing each step analysis, recording the used command lines and parameters and the log results generated during the operation, and once the program runs incorrectly, being able to quickly check the error.

Description

technical field [0001] The invention relates to the field of high-throughput sequencing, in particular to an automatic analysis method for prokaryotic transcriptome based on next-generation sequencing. Background technique [0002] Prokaryotic transcriptome sequencing is based on the second-generation high-throughput sequencing platform, constructing a chain-specific library to study all mRNAs transcribed by prokaryotes at a certain period or under certain environmental conditions, and obtaining prokaryotic genes from the sequence level and expression level All sequence information of organisms in a certain period or under certain environmental conditions. Since prokaryotic mRNA does not have a polyA tail structure, rRNA needs to be removed to obtain mRNA. [0003] The sequencing of prokaryotic transcriptomes is used to study all mRNAs transcribed by prokaryotic organisms in a certain period or under certain environmental conditions. With the decrease of sequencing cost an...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G16B20/30
CPCG16B20/30
Inventor 王玲平王智健姜丽荣沈立孙子奎
Owner 南京派森诺基因科技有限公司
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