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Decipher sequencing data with file formats for NGS

Next-generation sequencing (NGS) technologies generate tremendous amount of data. A typical human genome consists of ~3 billion base pairs to be sequenced. A critical step in NGS is to extract the information, stock it and transmit it in an easy-to-use and lightweight way. Why need file format? Coded in bits, a human genome would “only” weight about 700 MB (Reid Robison). However, sequencers generate short reads that redundantly span the sequence and then need to be aligned to a reference genome. Moreover, since sequencing is not perfect, every base has a score attached to it to evaluate the quality of sequencing. Thus, file formats have been developed to code a maximum of this information in a minimum of space. Here …

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How to identify the right tools for biological data analysis

In the biology big data context, managing the amount and diversity of data that experiments produce is a challenging task. Depending on the scope of your research, you probably spend a lot of your time searching for the right bioinformatics tools.   Like most, you probably have a general idea of how to analyze your data and have used more than one tool. If you’re working in a computational biology laboratory, you’ve probably heard the question “What is the best software for genome sequence alignment?” or “What algorithm is the standard for sequence alignment in genetics?” While BLAST is probably the most popular tool for this, there are lots of other tools for mining, and aligning biological data.  So choosing the right solution for …

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How to run proteomics analysis with mass-spectrometry

Proteins are an essential component of living organisms. In the systems biology era, the large-scale analysis of proteins and proteomes has a lot of applications, such as identification and quantification of proteins, study of post-translational modifications, protein structure, protein-protein or protein-nucleic acid interactions.   Here, we will focus on mass-spectrometry, the leading technology for high-throughput proteomics, and how it is used for protein characterization.  High-throughput proteomics Solving the complexity of gene expression at the whole-organism level with genomics and transcriptomics was thought to be the key to understanding the processes of life. However, protein expression does not always correlate with gene expression because mRNA is not always translated into protein, because a single transcript can code for several proteins, and …

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Virtualize your computing with IaaS

Since the advent of high-throughput sequencing, the number and complexity of biological data has exploded. Though information technology and computers have paralleled this development, researchers rarely meet the computational power and storage capability required to perform the analysis of their data (Ben Langmead and Abhinav Nellore). Infrastructure as a service to the rescue For this, infrastructures as a service (IaaS) have been created to let users run large-scale computing workloads on the cloud – that is, on virtual machines hosted on dedicated infrastructures – and to stock up to exabits of data.   According to the National Institute of Standards and Technology, IaaS can be described as:   The capability provided to the consumer is to provision processing, storage, networks, …

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How to find bioinformatics jobs

As part of your market strategy, you should craft and maintain a professional online persona. Use a platform such as LinkedIn or ResearchGate to create a detailed profile emphasizing key skills and experience, and to link up with others in relevant organizations or fields of research (…) Use online technical forums to ask about skills and experience needed in an industry  (…) Taking part in such dialogues can make recruiters notice you and seek you out regarding prospective openings. Peter Fiske. Why scientists need to market themselves. Nature.   As a job seeker, you probably use solutions to find job opportunities in your field of expertise. It can be difficult and time consuming to manually vet the many options available …

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Track and control your code with version control systems

Software codes are constantly evolving, become more complex as newer versions are released. But sometimes errors and bugs occur and being able to retrieve the latest stable version of your software code can be a life-saver. For this, most software code repositories are equipped with version control systems (VCS). Why do you need version control and how is it implemented? Software developers working in teams are continually writing new source code and changing existing source code. The code for a project is typically organized in a folder structure or “file tree”. One developer on the team may be working on a new feature while another developer fixes an unrelated bug by changing code, each developer may make their changes in …

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Best bioinformatics software for RNA-seq quantification and differential expression

RNA-sequencing is progressively replacing microarrays for the study of transcriptomes, and comparison of gene expression. One advantage of this technique is the ability to identify and quantify the expression of isoforms and unknown transcripts. To help you perform your experiments in the best conditions, we are closing our series of surveys on RNA-sequencing by asking the OMICtools community to choose the best quantification and differential expression tools.   1. DESeq 2. Limma 3. EdgeR RNA quantification and differential expression While microarrays produce a numerical estimate of the relative expression of genes across the genome, RNA-sequencing experiments rely on read-count distributions. After mapping reads to a reference genome, the expression level for each gene or isoform are estimated and normalized, and finally …

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Document your research with electronic lab notebooks

Laboratory notebook are an essential component of the scientific research process. They are used to document hypotheses, experiments and results, and can also serve a role in protecting intellectual property, among many other functions. However, their use is limited when a large number of researchers are working on a same project, and pasting digital results in the era of big data can be challenging. Electronic lab notebook to the rescue Electronic lab notebooks (ELNs) were first adopted by the pharmaceutical industry, and are now progressively (but slowly) entering the academic research area. Now several open-source and commercial solutions are proposed to researchers. There main advantages include long-term storage, optimization of data reproducibility, support for collaboration and sharing, and the ability …

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