CN106021995A - Graphical evaluation method of DNA (Deoxyribose Nucleic Acid) targeted sequencing cover degree - Google Patents
Graphical evaluation method of DNA (Deoxyribose Nucleic Acid) targeted sequencing cover degree Download PDFInfo
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- CN106021995A CN106021995A CN201610318269.3A CN201610318269A CN106021995A CN 106021995 A CN106021995 A CN 106021995A CN 201610318269 A CN201610318269 A CN 201610318269A CN 106021995 A CN106021995 A CN 106021995A
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
Abstract
The invention provides a graphical evaluation method of a DNA (Deoxyribose Nucleic Acid) targeted sequencing cover degree. The graphical evaluation method comprises the following steps: 1) data extraction: extracting the sequencing depth data of each site which is contained in different gene areas in a gene list; 2) data merging: when a gene contains excess basic group sites, merging the sequencing depth data of N similar sites into a mean value; and 3) graphical evaluation: displaying the sequencing coverage situation of each site which is contained in different gene areas in the gene list. The graphical evaluation method not only can evaluate indexes including basic group contents and the like but also can evaluate the coverage situation of different gene areas and various types of statistics in multiple genes and samples, and also can vividly report an evaluation result in a graphical way.
Description
Technical field
The invention belongs to gene information data processing field, especially relate to a kind of DNA target to order-checking
The graphical appraisal procedure of coverage.
Background technology
High throughput sequencing technologies is the most ripe, and time and expense needed for order-checking the most greatly reduce,
Therefore, the research quantity applying this technology for detection genovariation also gets more and more.But high-flux sequence
Technology is not perfect, owing to fragment to be measured is expanded by its PCR means to be passed through before order-checking
Increase, therefore add the mistake of order-checking.When having taken original sequencing data, sequencing quality is commented
Estimate and be just particularly important.Generally, obtaining sequencing data, the first step does quality control exactly, at this
One step has the software of many to use, such as FastQC, and it can divide from G/C content, sequence length
Sequencing data is estimated by cloth etc. aspect.But, this simply assesses order-checking from general level
Whether data have reached to support the requirement of subsequent analysis.
The only exon to gene such as the order-checking of exon group, gene chip order-checking carries out capture order-checking, often
Secondary order-checking can relate to many genes.Common quality evaluation software can only be in general level assessment order-checking matter
The quality of amount.When paying close attention to the sequencing quality assessment of some concrete gene or assessing gene chip at each
During capture level on gene, overall sequencing quality assessment cannot reflect exactly and focuses particularly on
The sequencing quality of gene.
Summary of the invention
In view of this, the present invention proposes a kind of DNA target to the order-checking graphical appraisal procedure of coverage, no
Only assess the indexs such as base contents, also include the assessment of gene zones of different coverage condition, and at many bases
Multiple statistics in cause, multisample, the mode graphically changed reports assessment result visually.
For reaching above-mentioned purpose, the technical scheme is that and be achieved in that: a kind of DNA target is to survey
The graphical appraisal procedure of sequence coverage, comprises the following steps:
1) data are extracted, and are used for extracting the order-checking depth data being included in gene zones of different each site interior；
2) data merge, when running into base position that gene comprises and being too much, by close N number of site
Order-checking depth data merges into average；
3) figure is shown, shows the order-checking in the gene zones of different being included in list of genes each site interior
Coverage condition.
Further, described step 1) information that inputs is bed file and order-checking depth data file depth
File, described bed file comprises chromosome number, gene initiation site, gene end site, gene name
Annotating with gene region, described depth file comprises chromosome number, chromosomal foci and the order-checking degree of depth.
Further, described bed file comprises the flanking region of gene, exon 1 and intron district,
It is required for the targeting order-checking targeted region i.e. exon of gene and the zones of different of gene is carried out position
The extraction of dot information, then corresponding site is carried out by the order-checking depth data in recycling depth file
The annotation of the order-checking degree of depth.
Further, step 3) information that inputs includes step 1), 2) data that obtain and from bed
The list of genes extracted in file, exports picture file, and the different piece of picture represents the not same district of gene
Territory.
Further, picture file only shows the exon of gene, and the different piece of picture represents difference
Exon.
Relative to prior art, a kind of DNA target of the present invention is graphically assessed to order-checking coverage
Method has the advantage that
The present invention is with output result (bed file and the order-checking degree of depth of common exon group order-checking flow processing
Data file) as input, based on sequencing data being processed the order-checking depth data that obtains and gene not
With region annotate data, complete extraction and the integration of data, present exon group order-checking to individual gene outside
The coverage condition of aobvious son, finally shows the order-checking depth profile situation of each gene with the form of picture.
The present invention not only assesses the indexs such as base contents, also includes the assessment of gene zones of different coverage condition, and
Its multiple statistics in polygenes, multisample, the mode graphically changed reports assessment result visually,
Reflect the sequencing quality of concrete concerned gene exactly.
Accompanying drawing explanation
The accompanying drawing of the part constituting the present invention is used for providing a further understanding of the present invention, the present invention's
Schematic description and description is used for explaining the present invention, is not intended that inappropriate limitation of the present invention.?
In accompanying drawing:
Fig. 1 is the schematic flow sheet of the present invention.
Detailed description of the invention
It should be noted that the feature in the case of not conflicting, in embodiments of the invention and embodiment
Can be mutually combined.
Describe the present invention below with reference to the accompanying drawings and in conjunction with the embodiments in detail.
As it is shown in figure 1, the step of the present invention is as follows:
1, data are extracted
Extracting the order-checking depth data being included in gene zones of different each site interior, input information includes
Bed file, this document comprise chromosome number, gene initiation site, gene end site, gene name and
Gene region annotates, and also includes the depth data file (depth file) that checks order, and this document comprises dyeing
Body number, chromosomal foci and the order-checking degree of depth.
When bed file comes from exon group sequencing data, it just only includes chromosome number, gene rises
Beginning site, gene end site and gene name, do not include that gene region annotates, and needs outside artificial interpolation aobvious
Son numbering is to show differentiation, and the information that exports also is slightly different, and no longer includes gene region annotation information,
But include the numbering of gene extron.
2, data merge
When running into base position that gene comprises and being too much, can be by the order-checking degree of depth in close N number of site
Data merge into average.The number in the site that will merge.Concrete value can be according to range file
Size determine.When range file is excessive, can suitably N value be arranged big the most a bit, otherwise
Speed and the quality of final picture of mapping can be affected and present effect.
3, figure is shown
Show the order-checking coverage condition in the gene zones of different being included in list of genes each site interior.Defeated
Go out the form of file, pdf or svg.Each output file may comprise multiple gene, therefore scheme
Sheet may be exactly a pattern matrix.The first width figure at each output file is legend, is followed by other
The order-checking coverage condition of each gene.
If simply showing the exon of gene, there is no legend, simply showing by two kinds of color interval and representing not
Same exon region.
The foregoing is only presently preferred embodiments of the present invention, not in order to limit the present invention, all at this
Within the spirit of invention and principle, any modification, equivalent substitution and improvement etc. made, should be included in
Within protection scope of the present invention.
Claims (5)
1. a DNA target is to the order-checking graphical appraisal procedure of coverage, it is characterised in that include following
Step:
1) data are extracted, and are used for extracting the order-checking depth data being included in gene zones of different each site interior；
2) data merge, when running into base position that gene comprises and being too much, by close N number of site
Order-checking depth data merges into average；
3) figure is shown, shows the order-checking in the gene zones of different being included in list of genes each site interior
Coverage condition.
A kind of DNA target the most according to claim 1 to the order-checking graphical appraisal procedure of coverage,
It is characterized in that, described step 1) information that inputs is bed file and order-checking depth data file depth
File, described bed file comprises chromosome number, gene initiation site, gene end site, gene name
Annotating with gene region, described depth file comprises chromosome number, chromosomal foci and the order-checking degree of depth.
A kind of DNA target the most according to claim 2 to the order-checking graphical appraisal procedure of coverage,
It is characterized in that, described bed file comprises the flanking region of gene, exon 1 and intron district, needs
For the targeting order-checking targeted region i.e. exon of gene, the zones of different of gene is carried out site
The extraction of information, then corresponding site is surveyed by the order-checking depth data in recycling depth file
The annotation of the sequence degree of depth.
A kind of DNA target the most according to claim 1 to the order-checking graphical appraisal procedure of coverage,
It is characterized in that, step 3) information that inputs includes step 1), 2) data that obtain and from bed
The list of genes extracted in file, exports picture file, and the different piece of picture represents the not same district of gene
Territory.
A kind of DNA target the most according to claim 1 to the order-checking graphical appraisal procedure of coverage,
It is characterized in that, picture file only shows the exon of gene, the different piece of picture represent different outside
Aobvious son.
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| Application Number | Priority Date | Filing Date | Title |
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| CN201610318269.3A CN106021995A (en) | 2016-05-13 | 2016-05-13 | Graphical evaluation method of DNA (Deoxyribose Nucleic Acid) targeted sequencing cover degree |
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| Application Number | Priority Date | Filing Date | Title |
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| CN201610318269.3A CN106021995A (en) | 2016-05-13 | 2016-05-13 | Graphical evaluation method of DNA (Deoxyribose Nucleic Acid) targeted sequencing cover degree |
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Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101914628A (en) * | 2010-09-02 | 2010-12-15 | 深圳华大基因科技有限公司 | Method and system for detecting polymorphism locus of genome target region |
| WO2014149134A2 (en) * | 2013-03-15 | 2014-09-25 | Guardant Health Inc. | Systems and methods to detect rare mutations and copy number variation |
| CN104232649A (en) * | 2013-06-10 | 2014-12-24 | 深圳华大基因科技有限公司 | Genetic mutant and application of genetic mutant |
-
2016
- 2016-05-13 CN CN201610318269.3A patent/CN106021995A/en active Pending
Patent Citations (3)
| Publication number | Priority date | Publication date | Assignee | Title |
|---|---|---|---|---|
| CN101914628A (en) * | 2010-09-02 | 2010-12-15 | 深圳华大基因科技有限公司 | Method and system for detecting polymorphism locus of genome target region |
| WO2014149134A2 (en) * | 2013-03-15 | 2014-09-25 | Guardant Health Inc. | Systems and methods to detect rare mutations and copy number variation |
| CN104232649A (en) * | 2013-06-10 | 2014-12-24 | 深圳华大基因科技有限公司 | Genetic mutant and application of genetic mutant |
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Application publication date: 20161012 |
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