{"id":8882,"date":"2016-07-26T04:30:26","date_gmt":"2016-07-26T04:30:26","guid":{"rendered":"http:\/\/admin.acceleratingscience.com\/behindthebench\/?p=8882"},"modified":"2016-08-11T21:20:11","modified_gmt":"2016-08-11T21:20:11","slug":"how-to-create-a-gmidx-analysis-method","status":"publish","type":"post","link":"https:\/\/www.thermofisher.com\/blog\/behindthebench\/how-to-create-a-gmidx-analysis-method\/","title":{"rendered":"How to Create a GMIDX Analysis Method"},"content":{"rendered":"<p>A question that often comes up is: how do I create an analysis method in GMIDX software? And then the follow up: what is an analysis method, anyway?\u00a0Simply put, it is a collection of user-defined settings GMIDX uses to analyse forensic DNA samples. It essentially tells the software how to identify, size, genotype and assess peaks. So, lets go ahead and create one in the debut episode of Forensic Focus.<\/p>\n<p><iframe loading=\"lazy\" width=\"760\" height=\"428\" src=\"https:\/\/www.youtube.com\/embed\/oArn_pRs24Q?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p>In the software, access the GeneMapper IDX Manager from the tools menu. On the Analysis Methods tab, select New.<\/p>\n<p>You need to define a name in the general tab &amp; select a security group. The rest is optional. Now click on the Allele tab. First select what bins to use \u2013 this defines the alleles based on the STR kit you are using. To automatically use the stutter values defined in your panel, check the \u201cmarker-specific stutter\u201d check box. This setting is typically utilized for casework samples. But for reference or databasing samples, global filters are often used. To use this option, simply enter a percentage in the applicable boxes below.<\/p>\n<p>You can customize how GMIDX identifies and sizes peaks in the Peak Detector tab. Be sure to reference your lab\u2019s SOP or your STR kit User Guide to help decide what settings to use.\u00a0You can select the full Analysis Range to analyse all the data points collected by the CE, or you can specify a specific range.<\/p>\n<p>The Sizing Range allows you to set in base pairs your size standard range.\u00a0The Peak Amplitude Thresholds specify the RFU value for peak detection for each dye color. These settings should be set based on your lab\u2019s validated analytical thresholds.<\/p>\n<p>Pay special attention to the Normalization check box. It\u2019s selected by default, so be sure to deselect if you do not want to normalize your 3500 data.\u00a0The other settings in this tab are utilized during the peak detection process. These settings are a topic for another day!<br \/>\nThe settings in the Peak Quality tab won\u2019t modify how your data is analysed, but will define how the software assesses and flags the samples.<\/p>\n<p>The minimum peak height fields help identify potential allelic dropout. These settings can be used to flag alleles that fall under a stochastic threshold.\u00a0The Max peak height setting can be used to flag peaks over a specific RFU.<\/p>\n<p>The remaining fields in the Peak Quality tab can be used to identify sister allele imbalances, artifacts, loss of resolution and even potential mixed samples.\u00a0You can even decide if you want to detect spikes differently in your allelic ladders and samples.<\/p>\n<p>The weighting of flags is controlled in the SQ and GQ Settings tab. A value of 0 means the flag is not turned on, while a value of 1 is the highest weight.\u00a0Optimization of this tab is especially helpful when using the software as an expert system.<\/p>\n<p>For the software to properly check the autosomal and YSTR markers in a kit such as Globalfiler, you will need to change the AMEL Cross Check weight to a value of 0.3 or higher.<\/p>\n<p>You can also change the range values for Pass, Check and Low Quality for sample Sizing Quality and Genotype Quality.\u00a0Once your analysis method is set, simply hit save. And don\u2019t forget the help button if you need assistance!<\/p>\n<p>&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>A question that often comes up is: how do I create an analysis method in GMIDX software? And then the follow up: what is an analysis method, anyway?\u00a0Simply put, it is a collection of user-defined settings GMIDX uses to analyse forensic DNA samples. It essentially tells the software how to identify, size, genotype and assess<\/p>\n","protected":false},"author":129,"featured_media":8883,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"_kad_blocks_custom_css":"","_kad_blocks_head_custom_js":"","_kad_blocks_body_custom_js":"","_kad_blocks_footer_custom_js":"","_monsterinsights_skip_tracking":false,"_genesis_hide_title":false,"_genesis_hide_breadcrumbs":false,"_genesis_hide_singular_image":false,"_genesis_hide_footer_widgets":false,"_genesis_custom_body_class":"","_genesis_custom_post_class":"","_genesis_layout":"","_jetpack_newsletter_access":"","_jetpack_dont_email_post_to_subs":false,"_jetpack_newsletter_tier_id":0,"_jetpack_memberships_contains_paywalled_content":false,"_jetpack_memberships_contains_paid_content":false,"footnotes":""},"categories":[71,108],"tags":[204],"division":[],"class_list":{"0":"post-8882","1":"post","2":"type-post","3":"status-publish","4":"format-standard","5":"has-post-thumbnail","7":"category-forensics","8":"category-lab-tips-and-tricks","9":"tag-forensic-focus","10":"entry"},"_selected_authors":"","_selected_reviewers":"","acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO Premium plugin v27.8 (Yoast SEO v27.8) - https:\/\/yoast.com\/product\/yoast-seo-premium-wordpress\/ -->\n<title>How to Create a GMIDX Analysis Method - Behind the Bench<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/how-to-create-a-gmidx-analysis-method\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"How to Create a GMIDX Analysis Method\" \/>\n<meta property=\"og:description\" content=\"A question that often comes up is: how do I create an analysis method in GMIDX software? And then the follow up: what is an analysis method, anyway?\u00a0Simply put, it is a collection of user-defined settings GMIDX uses to analyse forensic DNA samples. It essentially tells the software how to identify, size, genotype and assess\" \/>\n<meta property=\"og:url\" content=\"https:\/\/www.thermofisher.com\/blog\/behindthebench\/how-to-create-a-gmidx-analysis-method\/\" \/>\n<meta property=\"og:site_name\" content=\"Behind the Bench\" \/>\n<meta property=\"article:publisher\" content=\"https:\/\/www.facebook.com\/thermofisher\" \/>\n<meta property=\"article:published_time\" content=\"2016-07-26T04:30:26+00:00\" \/>\n<meta property=\"article:modified_time\" content=\"2016-08-11T21:20:11+00:00\" \/>\n<meta property=\"og:image\" content=\"https:\/\/admin.acceleratingscience.com\/behindthebench\/wp-content\/uploads\/sites\/9\/2016\/07\/Forensic-Focus-1.jpg\" \/>\n\t<meta property=\"og:image:width\" content=\"1280\" \/>\n\t<meta property=\"og:image:height\" content=\"720\" \/>\n\t<meta property=\"og:image:type\" content=\"image\/jpeg\" \/>\n<meta name=\"author\" content=\"Thermo Fisher Scientific Support Staff\" \/>\n<meta name=\"twitter:card\" content=\"summary_large_image\" \/>\n<meta name=\"twitter:creator\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:site\" content=\"@thermofisher\" \/>\n<meta name=\"twitter:label1\" content=\"Written by\" \/>\n\t<meta name=\"twitter:data1\" content=\"Thermo Fisher Scientific Support Staff\" \/>\n\t<meta name=\"twitter:label2\" content=\"Est. reading time\" \/>\n\t<meta name=\"twitter:data2\" content=\"3 minutes\" \/>\n<script type=\"application\/ld+json\" class=\"yoast-schema-graph\">{\"@context\":\"https:\\\/\\\/schema.org\",\"@graph\":[{\"@type\":\"Article\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/#article\",\"isPartOf\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/\"},\"author\":{\"name\":\"Thermo Fisher Scientific Support Staff\",\"@id\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/#\\\/schema\\\/person\\\/4fd82a620872ec4728c626c253335995\"},\"headline\":\"How to Create a GMIDX Analysis Method\",\"datePublished\":\"2016-07-26T04:30:26+00:00\",\"dateModified\":\"2016-08-11T21:20:11+00:00\",\"mainEntityOfPage\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/\"},\"wordCount\":573,\"commentCount\":0,\"image\":{\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/#primaryimage\"},\"thumbnailUrl\":\"https:\\\/\\\/admin.acceleratingscience.com\\\/behindthebench\\\/wp-content\\\/uploads\\\/sites\\\/9\\\/2016\\\/07\\\/Forensic-Focus-1.jpg\",\"keywords\":[\"forensic focus\"],\"articleSection\":[\"Forensics\",\"Lab Tips and Tricks\"],\"inLanguage\":\"en-US\",\"potentialAction\":[{\"@type\":\"CommentAction\",\"name\":\"Comment\",\"target\":[\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/#respond\"]}]},{\"@type\":\"WebPage\",\"@id\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/\",\"url\":\"https:\\\/\\\/www.thermofisher.com\\\/blog\\\/behindthebench\\\/how-to-create-a-gmidx-analysis-method\\\/\",\"name\":\"How to Create a GMIDX Analysis Method - 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