CN109616154A - The antidote and device of depth is sequenced - Google Patents
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- CN109616154A CN109616154A CN201811614856.2A CN201811614856A CN109616154A CN 109616154 A CN109616154 A CN 109616154A CN 201811614856 A CN201811614856 A CN 201811614856A CN 109616154 A CN109616154 A CN 109616154A
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Abstract
The present invention provides a kind of antidotes and device that depth is sequenced, wherein above-mentioned apparatus includes: acquisition module, for obtaining the sequencing depth of all sites of the G/C content in each site and the genome on genome；Division module, for all sites to be divided into N number of different sections according to specified rule according to the G/C content in each site, wherein N is positive integer；Determining module, for determining the weight of different sequencing depth in each section according to the sequencing depth in site in each section and the average sequencing depth in N number of section；Depth multiplied by weight corresponding with each sequencing depth, the sequencing depth in each site after being corrected will be sequenced for being directed to each site of the genome in processing module respectively.
Description
Technical field
The present invention relates to the communications fields, in particular to a kind of antidote and device that depth is sequenced.
Background technique
It is some studies have shown that by expand and be sequenced introduce GC deviation the sensibility of chromosomal aneuploidy is produced
Restriction effect.Under the conditions of different sequencings, such as agent formulations are different, sequencing temperature is different or cluster density is different, GC deviation
It may be introduced in sample preparation and sequencing procedure, this will lead to the survey for the genome area that G/C content is excessively high or G/C content is too low
Ordinal number is according to there is deviation.
The calculation method for eliminating GC deviation is developed in the related technology.HC Fan and SR Quake develop one kind and pass through office
The calculation method of portion's polynomial regression fit (LOESS recurrence) eliminates GC deviation, and this method based on part genome GC by being contained
Amount gives weight to each GC density, to pass through the Reads number for correcting each region multiplied by respective weights.But this method
It may cause data slight distortion, the accuracy of meeting Interference Detection when calculating.
For in the related technology, the deviation of sequencing depth is eliminated by the calculation method of local polynomial regression fitting
The problems such as method is easy to appear data distortion, and as a result accuracy is poor, not yet proposes effective technical solution.
Summary of the invention
The embodiment of the invention provides a kind of antidotes and device that depth is sequenced, at least to solve to lead in the related technology
The calculation method of local polynomial regression fitting is crossed come the method for eliminating the deviation of sequencing depth, data distortion is easy to appear, ties
The problems such as fruit accuracy is poor.
According to one embodiment of present invention, a kind of apparatus for correcting that depth is sequenced is provided, comprising: obtain module, use
In the sequencing depth for obtaining all sites of the G/C content and genome in each site on genome；Division module is used
In all sites are divided into N number of different sections according to specified rule according to the G/C content in each site, wherein N is positive whole
Number；Determining module, for for determining institute according to the section mean depth in site in each section and the mean depth in N number of section
State the weight of different sequencing depth in each section；Processing module will be surveyed respectively for being directed to each site of the genome
Sequence depth multiplied by weight corresponding with each sequencing depth, the sequencing depth in each site after being corrected.
In embodiments of the present invention, the division module, for G/C content to be fallen in the siteization in the first range point in N
In the both ends section in a difference section；And G/C content is fallen in into the siteization in the second range point in intermediate section, wherein
Intermediate section is the number of loci except other sections in the both ends section, in first range in N number of different sections
Less than the number of loci in second range.
In embodiments of the present invention, the determining module is also used to determine according to the following formula in each section not
With the weight of sequencing depth:
W=λall/λi, wherein λiFor the section mean depth in i-th of section, W is the weight, λallFor N number of area
Between mean depth, i is positive integer.
In embodiments of the present invention, the determining module is also used to determine the section mean depth in the following manner:
By the total depth of all sites in section divided by the number in site in the section, the section mean depth is obtained.
In embodiments of the present invention, the determining module is also used to determine being averaged for N number of section in the following manner
Depth: by the total depth of all sites in the genome divided by the number in site in the genome, N number of section is obtained
Mean depth.
In embodiments of the present invention, described device, further includes: rectification module, for according to each site after correction
The G/C content in sequencing depth and each site corrects the GC preference in each site.
According to another embodiment of the invention, a kind of antidote that depth is sequenced is additionally provided, comprising: obtain gene
The sequencing depth of all sites of the G/C content in each site and the genome in group；According to the G/C content in each site
The all sites are divided into N number of different sections according to specified rule, wherein N is positive integer；According to site in each section
Section mean depth and the mean depth in N number of section determine the weight of different sequencing depth in each section；For described
Depth multiplied by weight corresponding with each sequencing depth will be sequenced, each of after being corrected in each site of genome respectively
The sequencing depth in site.
In embodiments of the present invention, all sites are divided into according to specified rule by N according to the G/C content in each site
A difference section, comprising: G/C content is fallen in into the siteization in the first range point in the both ends section in N number of different sections；It will
G/C content falls in the siteization in the second range point in intermediate section, wherein and intermediate section is in N number of different sections,
Except other sections in the both ends section, the number of loci in first range is less than the number of sites in second range
Mesh..
In embodiments of the present invention, it is determined according to the mean depth in the interval depth in site in each section and N number of section
The weight of different sequencing depth in each section, comprising: determine different sequencings in each section according to the following formula
The weight of depth: W=λall/λi, wherein λiFor the section mean depth in i-th of section, W is the weight, λallIt is described N number of
The mean depth in section, i are positive integer.
In embodiments of the present invention, for each site of the genome, depth will be sequenced respectively and each sequencing is deep
Corresponding multiplied by weight is spent, after the sequencing depth in each site after being corrected, the method also includes: after correction
The sequencing depth in each site and the G/C content in each site correct the GC preference in each site.
According to another embodiment of the invention, a kind of storage medium is additionally provided, meter is stored in the storage medium
Calculation machine program, wherein the computer program is arranged to execute the correction of sequencing depth described in any of the above item when operation
Method.
Through the invention, institute is determined according to the mean depth of the section mean depth in site in each section and N number of section
State the weight of different sequencing depth in each section；For each site of the genome, respectively by sequencing depth and each
The corresponding multiplied by weight of depth is sequenced, the sequencing depth in each site after being corrected solves by adopting the above technical scheme
The method for eliminating the deviation of sequencing depth by the calculation method of local polynomial regression fitting in the related technology, is easy to appear
The problems such as data distortion, as a result accuracy is poor, and then a kind of method that accuracy is high is improved to eliminate the deviation of sequencing depth.
Detailed description of the invention
The drawings described herein are used to provide a further understanding of the present invention, constitutes part of this application, this hair
Bright illustrative embodiments and their description are used to explain the present invention, and are not constituted improper limitations of the present invention.In the accompanying drawings:
Fig. 1 is the flow chart according to the antidote of the sequencing depth of the embodiment of the present invention；
Fig. 2 is the structural block diagram of the apparatus for correcting of sequencing depth according to an embodiment of the present invention；
Fig. 3 is another structural block diagram of the apparatus for correcting of sequencing depth according to an embodiment of the present invention；
Fig. 4 is the schematic diagram (one) of effect before the correction according to an embodiment of the present invention that depth is sequenced；
Fig. 5 is the schematic diagram (one) of effect after the correction according to an embodiment of the present invention that depth is sequenced；
Fig. 6 is the schematic diagram (two) of effect before the correction according to an embodiment of the present invention that depth is sequenced；
Fig. 7 is the schematic diagram (two) of effect after the correction according to an embodiment of the present invention that depth is sequenced.
Specific embodiment
Hereinafter, the present invention will be described in detail with reference to the accompanying drawings and in combination with Examples.It should be noted that not conflicting
In the case of, the features in the embodiments and the embodiments of the present application can be combined with each other.
It should be noted that description and claims of this specification and term " first " in above-mentioned attached drawing, "
Two " etc. be to be used to distinguish similar objects, without being used to describe a particular order or precedence order.
It in the related technology,, be to each to be predicted when data volume is very big during being corrected to sequencing depth
Data fitting is primary, and runing time is longer, computationally intensive, and Poisson distribution has been introduced into rectifying for sequencing depth by the embodiment of the present invention
During just, calculating process caused by poor fitting and over-fitting is avoided, is specifically detailed in following embodiment and preferred embodiment
Technical solution.
Embodiment 1
The embodiment of the invention provides a kind of antidote that depth is sequenced, Fig. 1 is the sequencing according to the embodiment of the present invention
The flow chart of the antidote of depth, as shown in Figure 1, comprising the following steps:
Step S102: the sequencing of all sites of the G/C content and genome in each site on genome is obtained
Depth；
Step S104: all sites are divided into according to specified rule by N number of not same district according to the G/C content in each site
Between, wherein N is positive integer；
Step S106: according to the section mean depth in site in each section and the determination of the mean depth in N number of section
The weight of different sequencing depth in each section；
Step S108: for each site of the genome, it is corresponding with each sequencing depth depth will to be sequenced respectively
Multiplied by weight, the sequencing depth in each site after being corrected.
It through the above steps, (and can according to the mean depth in the section mean depth in site in each section and N number of section
To be average sequencing depth) determine the different weights that depth are sequenced in each section；For each position of the genome
Point, respectively will corresponding with each sequencing depth multiplied by weight of sequencing depth, the sequencing depth in each site after being corrected,
By adopting the above technical scheme, it solves and is sequenced deeply by the calculation method that local polynomial regression is fitted to eliminate in the related technology
The problems such as method of the deviation of degree is easy to appear data distortion, and as a result accuracy is poor, and then improve a kind of side that accuracy is high
The deviation of depth is sequenced to eliminate for method, and using the calculation of Poisson distribution, arithmetic speed is fast.
It should be noted that the weight in each site in above-mentioned each section is not necessarily identical, the same same survey in section
The weight in the site of sequence depth is identical, so being that depth will be sequenced multiplied by the weight of corresponding sequencing depth in step S108.
Above-mentioned steps S104 can pass through following technical side in one alternate embodiment there are many implementation
Case is realized: G/C content is fallen in the siteization in the first range point in the both ends section in N number of different sections；G/C content is fallen in
Siteization point in second range is in intermediate section, wherein intermediate section is to remove the both ends in N number of different sections
Other sections in section, the number of loci in first range are less than the number of loci in second range, and the present invention is real
Applying the second range in example should refer to containing the more section GC of number of loci, and the first range should refer to containing
There is the section GC that number of loci is fewer, for genome, usual G/C content is relatively more in 20%~60% site, that is,
Say GC 20%~60% site be the second range site, remaining site position the first range site.
In embodiments of the present invention, the weight of different sequencing depth in each section: W=is determined according to the following formula
λall/λi, wherein λiFor the section mean depth in i-th of section, W is the weight, λallFor the average depth in N number of section
Degree, determines the section mean depth: by the total depth of all sites in section divided by site in the section in the following manner
Number, obtain the section mean depth；The mean depth in N number of section is determined in the following manner: by the gene
The total depth of all sites obtains the mean depth in N number of section, i is divided by the number in site in the genome in group
Positive integer.
Optionally, after step S108, following technical scheme can also be performed: according to the sequencing in each site after correction
The G/C content in depth and each site corrects the GC preference in each site, that is to say, that in embodiments of the present invention,
The sequencing depth that step S108 is obtained can be understood as a kind of information of intermediate state, wherein the phase of sequencing depth and G/C content
Guan Xing, referred to as GC preference (English abbreviation GC bias), G/C content are in DNA4 kind base, shared by guanine and cytimidine
Ratio is known as G/C content.
Through the above description of the embodiments, those skilled in the art can be understood that according to above-mentioned implementation
The method of example can be realized by means of software and necessary general hardware platform, naturally it is also possible to by hardware, but it is very much
In the case of the former be more preferably embodiment.Based on this understanding, technical solution of the present invention is substantially in other words to existing
The part that technology contributes can be embodied in the form of software products, which is stored in a storage
In medium (such as ROM/RAM, magnetic disk, CD), including some instructions are used so that a terminal device (can be mobile phone, calculate
Machine, server or network equipment etc.) execute method described in each embodiment of the present invention.
Embodiment 2
Additionally provide a kind of apparatus for correcting that depth is sequenced in the present embodiment, the device for realizing above-described embodiment and
Preferred embodiment, the descriptions that have already been made will not be repeated.As used below, predetermined function may be implemented in term " module "
The combination of the software and/or hardware of energy.It is hard although device described in following embodiment is preferably realized with software
The realization of the combination of part or software and hardware is also that may and be contemplated.
Fig. 2 is the structural block diagram of the apparatus for correcting of sequencing depth according to an embodiment of the present invention, as shown in Fig. 2, the device
Include:
Module 20 is obtained, for obtaining all sites of the G/C content in each site and the genome on genome
Sequencing depth；
The all sites are divided into N number of by division module 22 for the G/C content according to each site according to specified rule
Different sections, wherein N is positive integer；
Determining module 24, for deep according to the section mean depth in site in each section and the average sequencing in N number of section
Degree determines the weight of different sequencing depth in each section；
Processing module 26 respectively will sequencing depth and each sequencing depth for being directed to each site of the genome
Corresponding multiplied by weight, the sequencing depth in each site after being corrected.
Through the invention, institute is determined according to the average sequencing depth of the interval depth in site in each section and N number of section
State the weight of different sequencing depth in each section；For each site of the genome, respectively by sequencing depth and each
The corresponding multiplied by weight of depth is sequenced, the sequencing depth in each site after being corrected solves by adopting the above technical scheme
The method for eliminating the deviation of sequencing depth by the calculation method of local polynomial regression fitting in the related technology, is easy to appear
The problems such as data distortion, as a result accuracy is poor, and then improve a kind of method that accuracy is high to eliminate the deviation of sequencing depth,
And using the calculation of Poisson distribution, arithmetic speed is fast.
In embodiments of the present invention, the division module 22, for G/C content to be fallen in the siteization in the first range point
In the both ends section in N number of different sections；And G/C content is fallen in into the siteization in the second range point in intermediate section,
In, intermediate section is the site except other sections in the both ends section, in first range in N number of different sections
Number is greater than the number of loci in second range.
In embodiments of the present invention, the determining module 24 is also used to determine according to the following formula in each section
The weight of difference sequencing depth:
W=λall/λi, wherein λiFor the section mean depth in i-th of section, W is the weight, λallFor N number of area
Between average sequencing depth, wherein determine the section mean depth in the following manner: by the aggregate depth of all sites in section
Degree obtains the section mean depth divided by the number in site in the section；The flat of N number of section is determined in the following manner
Equal depth: by the total depth of all sites in the genome divided by the number in site in the genome, N number of area is obtained
Between mean depth.
Fig. 3 is another structural block diagram of the apparatus for correcting of sequencing depth according to an embodiment of the present invention, as shown in figure 3,
In the embodiment of the present invention, described device, further includes: rectification module 28, for the sequencing depth according to each site after correction
The GC preference in each site is corrected with the G/C content in each site.
It should be noted that the technical solution of above-described embodiment 1- embodiment 2 can be used in combination, can also individually make
With the embodiment of the present invention is not construed as limiting this.
It is illustrated below in conjunction with correction process of the preferred embodiment to above-mentioned sequencing depth, but is not used in and limits this hair
The technical solution of bright embodiment, mainly comprises the steps that
Step 1, the whole genome sequence that sample is obtained by high-flux sequence.
The sequence that sequencing obtains is compared step 2 with genome hg19, and comparison result removal, which compares, arrives repetitive sequence
With comparison to the sequence on multiple positions, the sequence non-fully compared is removed.
All sites are divided into 43 according to its G/C content by step 3, the G/C content for calculating each site on genome hg19
The G/C content that the section of Bin, intermediate Bin are 1%, the G/C content that the section of both ends Bin is 20%, wherein by genome according to
G/C content is divided into 43 Bin, and the depth of all sites obeys Poisson distribution on each Bin.
Step 4, using Samtools software (be also possible to other executable software) to all sites on genome into
Row depth analysis counts the sequencing depth information of all sites.
Step 5, for each GC Bin, the sequencing depth of all sites almost obeys Poisson distribution.It calculates separately every
The mean depth λ of one BiniThe mean depth λ of (i 1,2...n represents the 1st, 2...n Bin) and all Binall。
Step 6, for each Bin i, calculate weight Wi=λall/λi, then the depth of all sites in the Bin is multiplied
With the corresponding weight W of this BiniSequencing depth in the as Bin after all sites correction.
Step 7, with 100kb be a sliding window Bin, count genome on different windows Bin mean depth information.
Step 8, the G/C content for calculating each Bin, using G/C content as horizontal axis, mean depth is the longitudinal axis, draws same sample
Whether the GC distribution map for correcting front and back, the depth information for comparing correction front and back have GC preference.
Based on the technical solution of above-mentioned steps 1- step 8, as shown in figure 4, the sample on the upper side with G/C content to mean depth
It is corrected, as illustrated in figures 4-5, horizontal axis is the G/C content of each Bin to the result before and after correcting, and the longitudinal axis is each Bin
Mean depth.
As shown in fig. 6-7, mean depth is corrected with G/C content sample on the lower side, corrects result such as Fig. 6-of front and back
Shown in 7, horizontal axis is the G/C content of each Bin, and the longitudinal axis is the mean depth of each Bin.
Optionally, in the present embodiment, above-mentioned storage medium can include but is not limited to: USB flash disk, read-only memory (Read-
Only Memory, referred to as ROM), it is random access memory (Random Access Memory, referred to as RAM), mobile hard
The various media that can store program code such as disk, magnetic or disk.
Optionally, the specific example in the present embodiment can be with reference to described in above-described embodiment and optional embodiment
Example, details are not described herein for the present embodiment.
Obviously, those skilled in the art should be understood that each module of the above invention or each step can be with general
Computing device realize that they can be concentrated on a single computing device, or be distributed in multiple computing devices and formed
Network on, optionally, they can be realized with the program code that computing device can perform, it is thus possible to which they are stored
It is performed by computing device in the storage device, and in some cases, it can be to be different from shown in sequence execution herein
Out or description the step of, perhaps they are fabricated to each integrated circuit modules or by them multiple modules or
Step is fabricated to single integrated circuit module to realize.In this way, the present invention is not limited to any specific hardware and softwares to combine.
The foregoing is only a preferred embodiment of the present invention, is not intended to restrict the invention, for the skill of this field
For art personnel, the invention may be variously modified and varied.It is all within principle of the invention, it is made it is any modification, etc.
With replacement, improvement etc., should all be included in the protection scope of the present invention.
Claims (10)
1. a kind of apparatus for correcting that depth is sequenced characterized by comprising
Module is obtained, for obtaining the sequencing of all sites of the G/C content in each site and the genome on genome
Depth；
Division module, for all sites to be divided into N number of not same district according to specified rule according to the G/C content in each site
Between, wherein N is positive integer；
Determining module, for according to the determination of the mean depth of the section mean depth in site in each section and N number of section
The weight of different sequencing depth in each section；
It is corresponding with each sequencing depth depth will to be sequenced respectively for being directed to each site of the genome in processing module
Multiplied by weight, the sequencing depth in each site after being corrected.
2. the apparatus according to claim 1, which is characterized in that the division module, for G/C content to be fallen in the first model
Siteization point in enclosing is in the both ends section in N number of different sections；And G/C content is fallen in into the siteization in the second range point
In intermediate section, wherein intermediate section is in N number of different sections, except other sections in the both ends section, described the
Number of loci in one range is less than the number of loci in second range.
3. the apparatus according to claim 1, which is characterized in that the determining module is also used to determine according to the following formula
The weight of different sequencing depth in each section:
W=λall/λi, wherein λiFor the section mean depth in i-th of section, W is the weight, λallFor N number of section
Mean depth, i are positive integer.
4. the apparatus according to claim 1, which is characterized in that the determining module is also used to determine in the following manner
The section mean depth: by the total depth of all sites in section divided by the number in site in the section, the section is obtained
Mean depth.
5. the apparatus according to claim 1, which is characterized in that the determining module is also used to determine in the following manner
The mean depth in N number of section: by the total depth of all sites in the genome divided by site in the genome
Number, obtains the mean depth in N number of section.
6. the apparatus according to claim 1, which is characterized in that described device further include:
Rectification module, for according to the correction of the G/C content in the sequencing depth in each site after correction and each site
The GC preference in each site.
7. a kind of antidote that depth is sequenced characterized by comprising
Obtain the sequencing depth of all sites of the G/C content and genome in each site on genome；
The all sites are divided into N number of different sections according to specified rule according to the G/C content in each site, wherein N is positive
Integer；
It is determined according to the mean depth of the section mean depth in site in each section and N number of section different in each section
The weight of depth is sequenced；
For each site of the genome, depth multiplied by weight corresponding with each sequencing depth will be sequenced respectively, obtain
The sequencing depth in each site after correction.
8. the method according to the description of claim 7 is characterized in that all sites are pressed according to the G/C content in each site
It is divided into N number of different sections according to specified rule, comprising:
G/C content is fallen in into the siteization in the first range point in the both ends section in N number of different sections；
G/C content is fallen in into the siteization in the second range point in intermediate section, wherein intermediate section is N number of not same district
Between in, except other sections in the both ends section, number of loci in first range is less than the position in second range
Point number.
9. the method according to the description of claim 7 is characterized in that according to the interval depth in site in each section and N number of area
Between mean depth determine in each section the weights of different sequencing depth, comprising:
The weight of different sequencing depth in each section is determined according to the following formula:
W=λall/λi, wherein λiFor the section mean depth in i-th of section, W is the weight, λallFor N number of section
Mean depth, i are positive integer.
10. will be sequenced respectively the method according to the description of claim 7 is characterized in that being directed to each site of the genome
Depth multiplied by weight corresponding with each sequencing depth, after the sequencing depth in each site after being corrected, the method
Further include:
The GC in each site is corrected according to the G/C content of the sequencing depth in each site after correction and each site
Preference.
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