Some of the local tools aim to produce static visualizations by using a set of genomic coordinates and commonly available programming languages like R or Shell script. Local (installable) tools run on the user’s machine and can import sequencing files which are stored in a secure location. exploration, documentation or the production of customized figures. Each of these tools serves a particular purpose, e.g. The visualization tools either produce static or dynamic (interactive) visualizations. To accomplish this, tools have been developed to support scientists without a programming background to visualize their datasets.
ICLIP RNA WINDOWS
Genomic windows are frequently visualized as stacked charts alongside the gene model. targets of RBPs in the case of iCLIP data. Īfter processing sequencing data, a common bioinformatician’s task is the visualization of genomic windows or genes of interest, i.e. Recently, we have adapted individual nucleotide resolution crosslinking immunoprecipitation (iCLIP) originally developed for mammals for the use in the reference plant Arabidopsis thaliana. To unravel posttranscriptional networks controlled by RBPs, RNAs associated with RBPs in vivo are recovered by immunoprecipitation of the RBP and high throughput sequencing of the co-precipitated RNAs. RNA-binding proteins (RBPs) play a key role in orchestrating the transcriptome at the posttranscriptional level. SEQing is customizable in many ways and has also the option to be secured by a password. The web-based access makes iCLIP data easily accessible, even with mobile devices. SEQing is written in Python3 and runs on Linux. Additionally, detailed information on the target genes can be incorporated in another tab. crossreferencing the iCLIP data with genes differentially expressed in mutants of the RBP and thus obtain some insights into a potential functional relevance of the binding sites. Moreover, SEQing supports RNA-seq data that can be displayed in a different window tab. Here we present SEQing, a customizable interactive dashboard to visualize crosslink sites on target genes of RNA-binding proteins that have been obtained by iCLIP. So far, no visualization tool exists that is easily accessible but also supports restricted access so that data can be shared among collaborators. Subsequently, the binding sites have to be visualized. These binding sites can be determined genome-wide through individual nucleotide resolution crosslinking immunoprecipitation (iCLIP). RNA-binding proteins interact with their target RNAs at specific sites.
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