scholarly journals Structural variation detection with read pair information --- An improved null-hypothesis reduces bias

2016 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Mattias Frånberg ◽  
Lars Arvestad
Keyword(s):  
Statistical Analysis ◽  
Fragment Length ◽  
Null Hypothesis ◽  
Structural Variation ◽  
False Positives ◽  
Simplified Model ◽  
Read Pair ◽  
New Model ◽  
Mate Pair ◽  
Reference Implementation

Abstract. Reads from paired-end and mate-pair libraries are often utilized to find structural variation in genomes, and one common approach is to use their fragment length for detection. After aligning read-pairs to the reference, read-pair distances are analyzed for statistically significant deviations. However, previously proposed methods are based on a simplified model of observed fragment lengths that does not agree with data. We show how this model limits statistical analysis of identifying variants and propose a new model, by adapting a model we have previously introduced for contig scaffolding, which agrees with data. From this model we derive an improved improved null hypothesis that, when applied in the variant caller CLEVER, reduces the number of false positives and corrects a bias that contributes to more deletion calls than insertion calls. A reference implementation is freely available at https://github.com/ksahlin/GetDistr.

scholarly journals Structural Variation Detection with Read Pair Information: An Improved Null Hypothesis Reduces Bias

2017 ◽  
Vol 24 (6) ◽  
pp. 581-589 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Mattias Frånberg ◽  
Lars Arvestad
Keyword(s):  
Null Hypothesis ◽  
Structural Variation ◽  
Read Pair

scholarly journals Genome scaffolding with PE-contaminated mate-pair libraries

2015 ◽  
Author(s):  
Kristoffer Sahlin ◽  
Rayan Chikhi ◽  
Lars Arvestad
Keyword(s):  
Source Code ◽  
Linear Programs ◽  
Read Pair ◽  
Insert Size ◽  
Essential Step ◽  
Genome Scaffolding ◽  
Mate Pair ◽  
A Genome ◽  
The Impact ◽  
Adapter Sequence

Scaffolding is often an essential step in a genome assembly process,in which contigs are ordered and oriented using read pairs from a combination of paired-ends libraries and longer-range mate-pair libraries. Although a simple idea, scaffolding is unfortunately hard to get right in practice. One source of problem is so-called PE-contamination in mate-pair libraries, in which a non-negligible fraction of the read pairs get the wrong orientation and a much smaller insert size than what is expected. This contamination has been discussed in previous work on integrated scaffolders in end-to-end assemblers such as Allpaths-LG and MaSuRCA but the methods relies on the fact that the orientation is observable, \emph{e.g.}, by finding the junction adapter sequence in the reads. This is not always the case, making orientation and insert size of a read pair stochastic. Furthermore, work on modeling PE-contamination has so far been disregarded in stand-alone scaffolders and the effect that PE-contamination has on scaffolding quality has not been examined before. We have addressed PE-contamination in an update of our scaffolder BESST. We formulate the problem as an Integer Linear Program (ILP) and use characteristics of the problem, such as contig lengths and insert size, to efficiently solve the ILP using a linear amount (with respect to the number of contigs) of Linear Programs. Our results show significant improvement over both integrated and standalone scaffolders. The impact of modeling PE-contamination is quantified by comparison with the previous BESST model. We also show how other scaffolders are vulnerable to PE-contaminated libraries, resulting in increased number of misassemblies, more conservative scaffolding, and inflated assembly sizes. The model is implemented in BESST. Source code and usage instructions are found at https://github.com/ksahlin/BESST. BESST can also be downloaded using PyPI.

scholarly journals Recommendations for statistical analysis involving null hypothesis significance testing

2020 ◽  
Vol 19 (5) ◽  
pp. 561-568 ◽  
Author(s):  
Andrew J. Harrison ◽  
Stuart A. McErlain-Naylor ◽  
Elizabeth J. Bradshaw ◽  
Boyi Dai ◽  
Hiroyuki Nunome ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Null Hypothesis ◽  
Significance Testing ◽  
Null Hypothesis Significance Testing

An Empirical Study of the Timbre Differences between Gut Core and Metal Core Violin “A” Strings

1973 ◽  
Vol 23 (3) ◽  
pp. 36-37
Author(s):  
Homer Garretson
Keyword(s):  
Statistical Analysis ◽  
Empirical Study ◽  
Null Hypothesis ◽  
Random Order ◽  
Response Sheet ◽  
Metal Core ◽  
Universities And Colleges ◽  
Controlled Conditions

The purpose of this study was to ascertain whether violinists and violists are able to aurally distinguish tonal differences between these two types of “A” strings. A series of musical examples were constructed to demonstrate different phases of string usage. These short phrases were then recorded under controlled conditions using both gut-core and metal-core “A” strings. The examples were then arranged in random order on magnetic tapes. On a simple response sheet, violinists and violists from ten universities and colleges were asked to identify which type of “A” string they were hearing. The statistical analysis of this material showed that in 3650 observations, 48.54 percent were correct. Since any value below 50 percent casts no doubt on the null hypothesis, it can be inferred from this study that there is no significant timbre difference observable between the two types.

The Controversy over Null Hypothesis Significance Testing Revisited

Methodology ◽  
2005 ◽  
Vol 1 (2) ◽  
pp. 55-70 ◽  
Author(s):  
Nekane Balluerka ◽  
Juana Gómez ◽  
Dolores Hidalgo
Keyword(s):  
Statistical Analysis ◽  
Null Hypothesis ◽  
Task Force ◽  
Data Interpretation ◽  
Psychological Research ◽  
Significance Testing ◽  
Null Hypothesis Significance Testing ◽  
Research Activity ◽  
Testing Hypotheses ◽  
Rigorous Research

Abstract. Null hypothesis significance testing (NHST) is one of the most widely used methods for testing hypotheses in psychological research. However, it has remained shrouded in controversy throughout the almost seventy years of its existence. The present article reviews both the main criticisms of the method as well as the alternatives which have been put forward to complement or replace it. It focuses basically on those alternatives whose use is recommended by the Task Force on Statistical Inference (TFSI) of the APA ( Wilkinson and TFSI, 1999 ) in the interests of improving the working methods of researchers with respect to statistical analysis and data interpretation. In addition, the arguments used to reject each of the criticisms levelled against NHST are reviewed and the main problems with each of the alternatives are pointed out. It is concluded that rigorous research activity requires use of NHST in the appropriate context, the complementary use of other methods which provide information about aspects not addressed by NHST, and adherence to a series of recommendations which promote its rational use in psychological research.

Calibration and statistical analysis of a simplified model for the anaerobic digestion of solid waste

2009 ◽  
Vol 30 (14) ◽  
pp. 1575-1584 ◽  
Author(s):  
Tine Daels ◽  
Bernard Willems ◽  
Han Vervaeren ◽  
Pascal Dejans ◽  
Guy Maes ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Anaerobic Digestion ◽  
Solid Waste ◽  
Simplified Model

scholarly journals The impact of the use of the cognitive map in the collection of material teaching methods for students of the Faculty of Fine Arts

2018 ◽  
Vol 212 (2) ◽  
pp. 291-320
Author(s):  
Dr. Salah Rahif
Keyword(s):  
Statistical Analysis ◽  
Teaching Methods ◽  
Null Hypothesis ◽  
Fine Arts ◽  
Cognitive Map ◽  
Teaching Material ◽  
Control Group ◽  
The Impact ◽  
Experimental Group

The present study aimed to - Effect of the cognitive map in the collection of material teaching methods. To achieve the aim of the research was the formulation of the null hypothesis of the following: 1 There are no statistically significant differences between the average scores of the experimental group students who are studying according to the cognitive map, and the average scores of the control group students who are studying under way in the collection of the usual methods of teaching material.     It reached the current research sample (80) students, the rate of (40) Talibautalbh the experimental group and (40) students of the control group .lam academic 2013-2014, Faculty of Fine Arts, University of Baghdad To achieve the aim of the research were carried out as follows: - Building a test consists of a written dimensionally (20) paragraph probationary After confirming the veracity of the test and persistence and conducting statistical analysis needed.

scholarly journals Statistical Analysis of Students’ Feedback with the Services of the on Campus Boy’s Hostels: A Case Study of Mehran University, Jamshoro

2019 ◽  
pp. 1-8
Author(s):  
Muteeullah Memon ◽  
Shahzaib Ahmed ◽  
Muhammad Waleed ◽  
Kazim Ali Korejo ◽  
Muhammad Ahsan Qadeer
Keyword(s):  
Social Sciences ◽  
Statistical Analysis ◽  
Water Supply ◽  
Null Hypothesis ◽  
Strong Relationship ◽  
First Aid ◽  
University Management ◽  
The University

Currently, the hostel life is so necessary for the students. During their higher studies, the students face a lot of problems of accommodation. After the solution of accommodation, the students face the issues in the hostels regarding their provided services. The data of students’ feedback is gathered from the Director MIS, MUET, Jamshoro by taking the sample of 60 students from each boy’s hostel. For analysis, we use the tool Statistical Package for Social Sciences (SPSS V.16). This study revealed the analysis of two services, water supply and first aid in the seven boy’s hostels of MUET, Jamshoro. The null hypothesis is accepted for all hostels except Rashidi, Hyder Bux Jatoi and Shah Abdul Latif. These results determined the strong relationship between the services water supply and first aid. From this study, we suggest to authorities of the university management to provide the necessary betterment regarding the water supply and first aid facilities in Rashidi, Hyder Bux Jatoi and Shah Abdul Latif hostels.

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