RNAseq

Best bioinformatics software for RNA-seq quality control

RNA-sequencing (RNA-seq) is currently the leading technology for transcriptome analysis. RNA-seq has a wide range of applications, from the study of alternative gene splicing, post-transcriptional modifications, to comparison of relative gene expression between different biological samples. To help you prepare and analyse your RNA-seq experiments under the best conditions, we have launched a new series of surveys focused on the best tools for each fundamental step of an RNA-seq experiment. Starting your analysis with quality control The first step in the analysis of an RNA-seq experiment is quality control. This crucial step will ensure that your data are of the best quality to perform the subsequent steps of your analysis. Quality control usually includes sequence quality, sequencing depth, reads duplication rates (clonal reads), …

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Best bioinformatics software for gene clustering

  Clustering is a fundamental step in the analysis of biological and omics data. It is used to construct groups of objects (genes, proteins) with related function, expression patterns, or known to interact together. In microarrays or RNA-seq experiments, gene clustering is often associated with heatmap representation for data visualization.   Choosing the right clustering tool for your analysis   Many clustering methods and algorithms have been developed and are classified into partitioning (k-means), hierarchical (connectivity-based), density-based, model-based and graph-based approaches. To help you choose between all the existing clustering tools, we asked OMICtools community to choose the best software. Here are the top 3 tools, chosen by 23 voters.   1. ClustEval 2. Babelomics 3. Altanalyze First place for …

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Single-cell RNA sequencing in immunology

Single-cell RNA sequencing (scRNA-seq) has revolutionized the study of the immune system and now has a wide range of applications in immunology. This technology spans the whole genome and provides an unbiased gene expression profile of individual cells. Bulk vs single-cell RNA-seq Traditional bulk RNA-seq is often performed on well-identified groups of cells thought to be homogeneous. However, quantification of molecular changes is made by estimating the mean value from millions of cells and averaging the signal of individual cells, thus ignoring cell-to-cell heterogeneity, which is a hallmark of adaptive immune cell subsets such as B and T lymphocytes. The need to identify new and discrete immune cell populations and to understand molecular changes that occur at the single cell level …

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CircRNAs in human and mouse tissues

Leng Han and Chunjiang He are the creators of the tissue-specific circular RNA (circRNA) database TSCD. They performed the first global analysis of tissue-specific circRNAs and collected these data in a comprehensive database. Here, they talk about their work and how the TSCD database can help researchers explore their RNA sequencing data. A repository of more than 300,000 tissue-specific RNAs With circRNAs attracting more attention in transcriptome research, we explored the global features of tissue-specific circRNAs in embryo development and organ differentiation. To identify tissue specific circRNAs, 3 algorithms, CIRI, circRNA_finder and find_circ, were applied to RNA-seq data collected from the ENCODE project and the NCBI GEO database.   Based on the major types of circRNA, we identified more than 300,000 tissue-specific circRNAs in different tissues. Our …

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Best CRISPR/Cas9 software tools

The development of CRISPR-Cas9 systems has revolutionized genome engineering in living organisms. This novel technology opens up a new era in genomics, along with a wide range of applications. Several bioinformatics tools have recently been developed for researchers designing CRISPR/Cas9 experiments, and analyzing and evaluating CRISPR/Cas9 genome editing.   A few weeks ago, we asked OMICtools members to choose their top 3 CRISPR/Cas9 favorite tools among those most used by the scientific community. Here are the results of your votes.    1. CRISPR-GA, CROP-IT, CRISPRTarget tools 2. Zifit 3. Crass and MAGeCK First position for CRISPR-GA, CROP-IT and CRISPRTarget tools Three web applications came out equally on top – each voted as a number #1 tool by 45% of the users surveryed: CRISPR-GA (CRISPR …

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Guidelines for RNA-sequencing data analysis

Adaptation and translation by Sarah Mackenzie and Helene Perrin of the french articles on bioinfo-fr.net: « L’analyse de données RNA-seq: mode d’emploi » by Julien Delafontaine, Bioinformatician at Lausanne University, and « RNA-seq : plus de profondeur ou plus d’échantillons? » by Isabelle Stévant, PhD student in Bioinformatics at Geneva University.   High-throughput sequencing is currently producing massive quantities of data, which is often extremely difficult for biologists to analyze, and who thus look to bioinformaticians for help. From these tens of gigabytes of data, the biologist hopes to extract results which are statistically relevant (preferably with very small p-values!), biologically interpretable, and which justify the time and money invested in the study.   A biologist typically has multiple aims, such as: to …

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