Tag Archives: Bias

With rapid technical advances, single cell RNA-seq (scRNA-seq) has been used to detect cell subtypes exhibiting distinct gene expression profiles and to trace cell transitions in development and disease...

Next-generation sequencing technologies have revolutionized the study of small RNAs (sRNAs) on a genome-wide scale. However, classical sRNA library preparation methods introduce serious bias, mainly during adapter ligation steps. Several types...

Detecting sources of bias in transcriptomic data is essential to determine signals of Biological significance. Researchers from the University of London outline a novel method to detect sequence specific bias in short read Next Generation Sequencing data. This is based ...

Many biases and spurious effects are inherent in RNA-seq technology, resulting in a non-uniform distribution of sequencing read counts for each base position in a gene. Therefore, a base-level strategy is required to model the non-uniformity. Also, the properties of ...

Single cell RNA sequencing (scRNA-seq) has rapidly gained popularity for profiling transcriptomes of hundreds to thousands of single cells. This technology has led to the discovery of novel cell types and revealed insights into the development of complex tissues. However, ...

Accuracy of transcript quantification with RNA-Seq is negatively affected by positional fragment bias. Researchers at Lexogen GmbH introduce Mix2 (rd. “mixquare”), a transcript quantification method which uses a mixture of probability distributions to model and thereby neutralize the effects of positional ...

The recent emergence of alternative polyadenylation (APA) as an engine driving transcriptomic diversity has stimulated the development of sequencing methodologies designed to assess genome-wide polyadenylation events. The goal of these approaches is to enrich, partition, capture and ultimately sequence poly(A) ...

Low-input RNA-seq is powerful to represent the gene expression profiles with limited number of cells, especially when single-cell variations are not the aim. However, pre-amplification-based and molecule index-based library construction methods boost bias or require higher throughput. Here researchers at ...

Technique detects technical biases that otherwise confound test results A new computational method can improve the accuracy of gene expression analyses, which are increasingly used to diagnose and monitor cancers and are a major tool for basic biological research. Researchers ...

The recent success of deep learning techniques in machine learning and artificial intelligence has stimulated a great deal of interest among bioinformaticians, who now wish to bring the power of deep learning to bare on a host of bioinformatical problems. ...