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Bacteria ncRNA prediction method based on Illumina transcriptome sequencing data and PeakCalling method

A technology of transcriptome sequencing and prediction methods, applied in the field of bioinformatics

Active Publication Date: 2017-12-22
武汉生命之美科技有限公司
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Problems solved by technology

But so far the PeakCalling method has not been used for the prediction and analysis of ncRNA

Method used

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  • Bacteria ncRNA prediction method based on Illumina transcriptome sequencing data and PeakCalling method
  • Bacteria ncRNA prediction method based on Illumina transcriptome sequencing data and PeakCalling method
  • Bacteria ncRNA prediction method based on Illumina transcriptome sequencing data and PeakCalling method

Examples

Experimental program
Comparison scheme
Effect test

Embodiment 1

[0043] [Example 1] Obtaining the data to be analyzed of each transcriptome

[0044] We obtained the transcriptome data of a Yersinia pestis, the specific species information is Yersinia Pestis, and there are two transcriptome data: wild strain and knockout strain. For its RNA, first delete the rRNA inside, and then build the library, and then obtain the original sequencing data of the transcriptome of the two groups of rRNA deletion of a certain Yersinia pestis through the Illumina sequencing platform;

[0045] After obtaining the transcriptome sequencing data, filter the unqualified data in each group of raw sequencing data, the unqualified data includes: low-quality reads, wherein the low-quality reads include, more than 30% of the bases in the sequence are of low quality reads of less than 20; reads with a sequence length of less than 16 after trimming off the sequencing adapter; trimming of reads with a sequence length of less than 16 after low-quality base sequences, wher...

Embodiment 2

[0047] [Example 2] Peakcalling method to predict ncRNA of Yersinia pestis

[0048] Use the PeakCalling method to obtain the Peak schematic diagram, see figure 2 .

[0049] 1. Aligning the data to be analyzed of the two transcriptomes to the reference genome of Yersinia pestis;

[0050] Use bowtie or bowtie2 software for comparison. When using bowtie software for comparison, the specific parameters are set as follows: use -v parameter, allow 2 mismatches, and output 2 best matching results; when using bowtie2 for comparison, -N parameter Select 1, use --end-to-end comparison mode, set the number of threads when the program is running to 1~16; set the output file type to sam format.

[0051] 2. After obtaining the comparison results, use the genomecov method of bedtools to count the comparison depth of each position in the reference genome of each sample, perform quantitative analysis on the comparison depth of the whole genome, and select the -d parameter.

[0052] 3. Accor...

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Abstract

The invention belongs to the biological information technology field, and particularly relates to a non-coding RNA analysis prediction method combining a base fragment obtained by Illumina second-generation sequencing with PeakCalling method. The method comprises the steps of rejecting rRNA bacteria second-generation sequencing data; after obtaining the data, analyzing the data by conducting pollution removing and low quality removing analysis of the data to obtain Clean reads first; then comparing the reads onto a bacteria genome; predicting a transcription unit preliminarily; filtering noted mRNA and ncRNA to obtain predicted ncRNA; and noting the ncRNA to a known ncRNA database Rfam to obtain a final prediction result. The unnoted ncRNA in the bacteria genome can be predicted accurately, making up the insufficiency of experiment means, and providing a favorable support for anaphase experiment and scientific research.

Description

technical field [0001] The invention relates to the technical field of biological information, in particular to a bacterial ncRNA prediction method based on Illumina transcriptome sequencing data and the PeakCalling method. Background technique [0002] Since 2004, the next-generation sequencing technology has developed rapidly. The next-generation sequencing technology has the characteristics of being able to sequence hundreds of thousands to several million DNA molecules in parallel at one time, and the read length is relatively short. It provides a good technical means for scientific and medical research, and has a wide range of applications in genome assembly and gene expression. [0003] In 2006, Illumina Corporation of the United States proposed a self-developed genome analysis platform. The basic principle of sequencing is to synthesize and sequence at the same time. Due to its low requirements on sample quality, and its outstanding advantages such as high accuracy, ...

Claims

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Application Information

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Patent Type & Authority Applications(China)
IPC IPC(8): G06F19/18G06F19/20
CPCG16B20/00G16B25/00
Inventor 张翼陈栋程超
Owner 武汉生命之美科技有限公司
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