scholarly journals A tandem simulation framework for predicting mapping quality

2017 ◽  
Author(s):  
Ben Langmead
Keyword(s):  
Simulation Framework ◽  
Sequencing Data ◽  
Read Alignment ◽  
Data Analyses ◽  
True Point ◽  
General Method

AbstractRead alignment is the first step in most sequencing data analyses. Because a read’s point of origin can be ambiguous, aligners report a mapping quality: the probability the reported alignment is incorrect. Despite its importance, there is no established and general method for calculating mapping quality. We describe a framework for predicting mapping qualities that works by simulating a set of tandem reads, similar to the input reads in important ways, but for which the true point of origin is known. We implement this in an accurate and low-overhead tool called Qtip, which is compatible with popular aligners.

scholarly journals Assessing the reliability of spike-in normalization for analyses of single-cell RNA sequencing data

2017 ◽  
Author(s):  
Aaron T. L. Lun ◽  
Fernando J. Calero-Nieto ◽  
Liora Haim-Vilmovsky ◽  
Berthold Göttgens ◽  
John C. Marioni
Keyword(s):  
Single Cell ◽  
Rna Sequencing ◽  
Capture Efficiency ◽  
Cellular Heterogeneity ◽  
Sequencing Data ◽  
Constant Amount ◽  
Technical Noise ◽  
Data Analyses ◽  
Single Cell Rna Sequencing ◽  
The Cost

AbstractBy profiling the transcriptomes of individual cells, single-cell RNA sequencing provides unparalleled resolution to study cellular heterogeneity. However, this comes at the cost of high technical noise, including cell-specific biases in capture efficiency and library generation. One strategy for removing these biases is to add a constant amount of spike-in RNA to each cell, and to scale the observed expression values so that the coverage of spike-in RNA is constant across cells. This approach has previously been criticized as its accuracy depends on the precise addition of spike-in RNA to each sample, and on similarities in behaviour (e.g., capture efficiency) between the spike-in and endogenous transcripts. Here, we perform mixture experiments using two different sets of spike-in RNA to quantify the variance in the amount of spike-in RNA added to each well in a plate-based protocol. We also obtain an upper bound on the variance due to differences in behaviour between the two spike-in sets. We demonstrate that both factors are small contributors to the total technical variance and have only minor effects on downstream analyses such as detection of highly variable genes and clustering. Our results suggest that spike-in normalization is reliable enough for routine use in single-cell RNA sequencing data analyses.

scholarly journals A Comprehensive Evaluation of Single-end Sequencing Data Analyses for Environmental Microbiome Research

2021 ◽  
Author(s):  
Meganathan Ramakodi
Keyword(s):  
Sample Size ◽  
Comprehensive Evaluation ◽  
Illumina Miseq ◽  
Sequencing Data ◽  
Core Microbiome ◽  
Data Analyses ◽  
Illumina Miseq Platform ◽  
Microbiome Research ◽  
Miseq Platform ◽  
Sequencing Platforms

Abstract Illumina sequencing platforms have been widely used for amplicon-based environmental microbiome research. Analyses of amplicon data of environmental samples, generated from Illumina MiSeq platform illustrate the reverse (R2) reads in the PE datasets to have low quality towards the 3’ end of the reads which affect the sequencing depth of samples and ultimately impact the sample size which may possibly lead to an altered outcome. This study evaluates the usefulness of single-end (SE) sequencing data in microbiome research when the Illumina MiSeq PE dataset shows significantly high number of low quality reverse reads. In this study, the amplicon data (V1V3, V3V4, V4V5 and V6V8) from 128 environmental (soil) samples, downloaded from SRA, demonstrate the efficiency of single-end (SE) sequencing data analyses in microbiome research. The SE datasets were found to infer the core microbiome structure as comparable to the PE dataset. Conspicuously, the forward (R1) datasets inferred a higher number of taxa as compared to PE datasets for most of the amplicon regions, except V3V4. Thus, analyses of SE sequencing data, especially R1 reads, in environmental microbiome studies could ameliorate the problems arising on sample size of the study due to low quality reverse reads in the dataset. However, care must be taken while interpreting the microbiome structure as few taxa observed in the PE datasets were absent in the SE datasets. In conclusion, this study demonstrates the availability of choices in analyzing the amplicon data without having the need to remove samples with low quality reverse reads.

scholarly journals Prophage Tracer: precisely tracing prophages in prokaryotic genomes using overlapping split-read alignment

2021 ◽  
Author(s):  
Kaihao Tang ◽  
Weiquan Wang ◽  
Yamin Sun ◽  
Yiqing Zhou ◽  
Pengxia Wang ◽  
...  
Keyword(s):  
Performance Testing ◽  
Sequencing Data ◽  
Associated Bacteria ◽  
Read Alignment ◽  
Phage Gene ◽  
Short Read Sequencing ◽  
Split Read ◽  
Prokaryotic Genomes ◽  
Mining Tool ◽  
Gene Similarity

Abstract The life cycle of temperate phages includes a lysogenic cycle stage when the phage integrates into the host genome and becomes a prophage. However, the identification of prophages that are highly divergent from known phages remains challenging. In this study, by taking advantage of the lysis-lysogeny switch of temperate phages, we designed Prophage Tracer, a tool for recognizing active prophages in prokaryotic genomes using short-read sequencing data, independent of phage gene similarity searching. Prophage Tracer uses the criterion of overlapping split-read alignment to recognize discriminative reads that contain bacterial (attB) and phage (attP) att sites representing prophage excision signals. Performance testing showed that Prophage Tracer could predict known prophages with precise boundaries, as well as novel prophages. Two novel prophages, dsDNA and ssDNA, encoding highly divergent major capsid proteins, were identified in coral-associated bacteria. Prophage Tracer is a reliable data mining tool for the identification of novel temperate phages and mobile genetic elements. The code for the Prophage Tracer is publicly available at https://github.com/WangLab-SCSIO/Prophage_Tracer.

A General Method for Spectrometer Design in the Scoff Approximation

1976 ◽  
Vol 34 ◽  
pp. 538-539
Author(s):  
J. R. Fields
Keyword(s):  
Electron Microscope ◽  
Transmission Electron Microscope ◽  
Energy Analysis ◽  
Incident Beam ◽  
Scanning Transmission Electron Microscope ◽  
Chemical Identification ◽  
Scanning Transmission Electron ◽  
Transmission Electron ◽  
Scanning Transmission ◽  
General Method

The energy analysis of electrons scattered by a specimen in a scanning transmission electron microscope can improve contrast as well as aid in chemical identification. In so far as energy analysis is useful, one would like to be able to design a spectrometer which is tailored to his particular needs. In our own case, we require a spectrometer which will accept a parallel incident beam and which will focus the electrons in both the median and perpendicular planes. In addition, since we intend to follow the spectrometer by a detector array rather than a single energy selecting slit, we need as great a dispersion as possible. Therefore, we would like to follow our spectrometer by a magnifying lens. Consequently, the line along which electrons of varying energy are dispersed must be normal to the direction of the central ray at the spectrometer exit.

Phase behavior of cationic and anionic surfactants at low concentrations

1992 ◽  
Vol 50 (1) ◽  
pp. 694-695
Author(s):  
E. Naranjo
Keyword(s):  
Phase Behavior ◽  
Structural Characterization ◽  
Dynamic Systems ◽  
Anionic Surfactants ◽  
Intermolecular Forces ◽  
Stable Form ◽  
Surfactant Mixtures ◽  
Low Concentrations ◽  
Cationic And Anionic Surfactants ◽  
General Method

Equilibrium vesicles, those which are the stable form of aggregation and form spontaneously on mixing surfactant with water, have never been demonstrated in single component bilayers and only rarely in lipid or surfactant mixtures. Designing a simple and general method for producing spontaneous and stable vesicles depends on a better understanding of the thermodynamics of aggregation, the interplay of intermolecular forces in surfactants, and an efficient way of doing structural characterization in dynamic systems.

Compensatory Coping Through the Extension of Working Hours

2019 ◽  
Vol 63 (3) ◽  
pp. 115-128 ◽  
Author(s):  
Maie Stein ◽  
Sylvie Vincent-Höper ◽  
Nicole Deci ◽  
Sabine Gregersen ◽  
Albert Nienhaus
Keyword(s):  
Job Demands ◽  
Working Hours ◽  
Well Being ◽  
Leader Member Exchange ◽  
Workplace Health ◽  
High Quality ◽  
Data Analyses ◽  
Member Exchange ◽  
The Relationship ◽  
Advance Knowledge

Abstract. To advance knowledge of the mechanisms underlying the relationship between leadership and employees’ well-being, this study examines leaders’ effects on their employees’ compensatory coping efforts. Using an extension of the job demands–resources model, we propose that high-quality leader–member exchange (LMX) allows employees to cope with high job demands without increasing their effort expenditure through the extension of working hours. Data analyses ( N = 356) revealed that LMX buffers the effect of quantitative demands on the extension of working hours such that the indirect effect of quantitative demands on emotional exhaustion is only significant at low and average levels of LMX. This study indicates that integrating leadership with employees’ coping efforts into a unifying model contributes to understanding how leadership is related to employees’ well-being. The notion that leaders can affect their employees’ use of compensatory coping efforts that detract from well-being offers promising approaches to the promotion of workplace health.

Caricaturing as a general method to improve poor face recognition: Evidence from low-resolution images, other-race faces, and older adults.

2019 ◽  
Vol 25 (2) ◽  
pp. 256-279 ◽  
Author(s):  
Amy Dawel ◽  
Tsz Ying Wong ◽  
Jodie McMorrow ◽  
Callin Ivanovici ◽  
Xuming He ◽  
...  
Keyword(s):  
Older Adults ◽  
Face Recognition ◽  
Low Resolution ◽  
General Method ◽  
Low Resolution Images
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