![]() abl1, in the search box (on the top-left corner, arrow). We can navigate to a gene region by typing a gene symbol, e.g. The user can zoom in and out using the mouse wheel or zoom tool at the top right of the tool bar. The first time that tracks are added, it may take a few minutes while indexing is performed. The two new BAM tracks will appear at the bottom of the browser. In the Specify Track Source window, select Alignment track | Sorted BAM file.Ĭhoose the two BAM files, (RNA-Seq alignment) and (DNA-Seq alignment). First, go to Add Track | Add Track From Server File. In this tutorial we will add BAM files from a server drive. The BAM alignment track can display a variety of information such as coverage, exon junctions, pileup, profiles, sequences, and variations. A common task is to add alignment tracks, e.g. This section focuses on adding next generation sequencing data files (BAM files). NGS data sets, variable view of -omic data sets Data sets in Analysis tab of Array Studio, e.g.Affymetrix probes and probesets track, SNP Pre-built mapping tracks by Omicsoft, e.g.Tab-delimited text files containing genomic coordinate information columns (chromosome, start, end).If the user has connected to a server, the newly created genome browser will be a server genome browser, the window for creating a genome browser will be slightly different from creating a local genome browser, and the server genome browser will use reference genome from server (if your server already has that genome reference, you won't need to download it again).įor server genome browser, users can still add tracks from local files, but alignment file can't be shared (users can only share the genome browser when they are connected to the server).Īfter creating a new browser, the default browser window for the chromosome 1 is shown.Ī number of data types can be added as tracks including: The version of reference genome in the BAM file can be checked using Array Studio ( NGS | Tools | Bam Tools | Extract header and infer reference). If one intends to load a BAM alignment track, the reference in BAM headers has to match the one in the Genome Browser. Select the Human.B37.3 Reference and the OmicsoftGene20130723 gene model.Ĭlicking the Browse button allows the user to specify a location to save the Genome Browser: If the Reference or Gene model is not listed, the user can build one using Array Studio tools ( NGS | Build Reference or Gene Model). For more details on general functions and usage of the Genome Browser, please refer to the Genome Browser online help: link Create Genome BrowserĪ new browser can be created by choosing the New button on the toolbar, or by going to File | New Browser.Ī window will appear and allow the user to specify a reference genome build and gene model track to be loaded into the new browser. This tutorial mainly focuses on browsing next generation sequencing data and its integration with the analytical tools of Array Studio. To minimize the file size, we provide a subset of the alignment files containing regions of four genes: BCR, ABL1, NUP214 and XKR3: link RNA inter transcript fusion read pairs detected by ArrayStudio RNA fusion junction spanning reads detected by ArrayStudio Sample IDĭNA fusion junction spanning reads detected by ArrayStudioĭNA inter gene fusion read pairs detected by ArrayStudio This Genome Browser tutorial will cover the importing and visualizing six NGS alignment files generated from RNA-Seq and DNA-Seq tutorial. It is highly recommended that the users complete the prerequisite for this tutorial: RNA-Seq and DNA-Seq tutorial, as a way to learn the basics in sequencing data analysis. ![]() 64-bit mode can run much faster than 32-bit mode, and is highly recommended when there is no Array Server connection and alignment files are not indexed. The OmicSoft Genome Browser can visualize NGS data in 32-bit mode on a Windows 32-bit computer with 2GB of RAM minimum, or in 64-bit mode on a Windows 64-bit computer with 8GB of RAM. The Genome Browser tab can be found in Array Studio and Array Viewer software: OmicSoft's Genome Browser is fully integrated with Omicsoft's Array Suite package (Array Server and Array Studio). In the Omicsoft Genome Browser tutorial we will learn:
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