{"id":749,"date":"2016-06-07T10:41:20","date_gmt":"2016-06-07T14:41:20","guid":{"rendered":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/?page_id=749"},"modified":"2017-09-04T15:08:37","modified_gmt":"2017-09-04T19:08:37","slug":"tools","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/tools\/","title":{"rendered":"Tools"},"content":{"rendered":"<h1>DISC_gDNA_Generator<\/h1>\n<ul>\n<li>Takes an RNA sequence as input to generate a list of DNA guides for DISC mediated cleavage covering the length of the RNA.<\/li>\n<li>Download <a href=\"https:\/\/osu.box.com\/v\/gDNAgen-v1\">gDNAgen_v1.1.exe<\/a>\n<ul>\n<li>You will need to have Python2.x installed.<\/li>\n<li>Double-click on the *.exe file.<\/li>\n<li>Select a text file with your sequence.\n<ul>\n<li>The file will need to have only the sequence on the first line and nothing else in the document.<\/li>\n<\/ul>\n<\/li>\n<li>At the next prompt, type in the name of your desired output file without an extension (e.g. &#8220;output&#8221; will yield the file output.txt).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<h1><\/h1>\n<h1><strong>RiboCAT<\/strong><\/h1>\n<ul>\n<li><strong>RiboCAT<\/strong>\u00a0 &#8211; \u00a0(<strong><u>Ribo<\/u><\/strong>nucleic acid <strong><u>C<\/u><\/strong>apillary-electrophoresis <strong><u>A<\/u><\/strong>nalysis <strong><u>T<\/u><\/strong>ool):\u00a0A\u00a0new, user-friendly tool for analysis of RNA probing data collected using capillary electrophoresis.<\/li>\n<li><strong>RiboDOG<\/strong>\u00a0 &#8211; \u00a0(<strong><u>Ribo<\/u><\/strong>CAT <strong><u>D<\/u><\/strong>ata <strong><u>O<\/u><\/strong>utput <strong><u>G<\/u><\/strong>enerator): A companion tool for RiboCAT that formats outputs for error-checking and input files for RNAStructure.<\/li>\n<li>Please reference the following:\n<ul>\n<li>Cantara, W. A., Hatterschide, J., Wu, W. &amp; Musier-Forsyth, K. RiboCAT: a new capillary electrophoresis data analysis tool for nucleic acid probing. <em>RNA<\/em> <strong>23<\/strong>, 240-249, doi:10.1261\/rna.058404.116 (2017).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li><em><strong>Downloads<\/strong><\/em>\n<ul>\n<li><em>RiboCAT RNA Probing Tools<\/em>\n<ul>\n<li>Download <a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/10\/RiboCAT_v1.42.xlsb\">RiboCAT_v1.42<\/a>\u00a0(<em><strong>updated Oct 18,\u00a02016<\/strong><\/em>)\n<ul>\n<li>Due to new security rules, an additional installation step is required for Excel for Mac 2016 users (see User Manual for details) &#8211; Download script <a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/10\/RiboCATCallPython.scpt\">HERE<\/a>.<\/li>\n<\/ul>\n<\/li>\n<li>Download <a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/06\/RiboDOG_v1.20.xlsb\">RiboDOG_v1.20<\/a>\u00a0(<em><strong>updated Dec\u00a015,\u00a02016<\/strong><\/em>)\n<ul>\n<li>Some features not compatible with Excel for Mac 2016 (see User Manual for details)<\/li>\n<\/ul>\n<\/li>\n<li>Download\u00a0<a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/10\/UserManual_v06.pdf\">User_Manual<\/a>\/<a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/10\/QuickStartGuide_v09.pdf\">Quick_Start_Guide<\/a>\/<a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/10\/RiboCAT-StepByStep-v3.pdf\">Step-by-Step_Guide<\/a><\/li>\n<li>Download <a href=\"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-content\/uploads\/2016\/09\/Tutorial_Files.zip\">Tutorial_Files<\/a>\u00a0(requires unzipping software)<\/li>\n<li>\n<ul>\n<li>This works with Windows\u00a0and\u00a0Mac.<\/li>\n<li>RiboCAT requires Python 2.X, and it must be in your PATH.<\/li>\n<li>Report bugs to\u00a0<a href=\"mailto:willc.tools@gmail.com\">willc.tools@gmail.com<\/a><\/li>\n<\/ul>\n<\/li>\n<li>View the video tutorial below (<em><strong>updated Oct 18,\u00a02016<\/strong><\/em>; now with ability to navigate to different &#8220;chapters&#8221; of the tutorial):<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><iframe loading=\"lazy\" title=\"RiboCAT VideoTutorial (Updated 10\/17\/2016)\" width=\"710\" height=\"399\" src=\"https:\/\/www.youtube.com\/embed\/xemW2h9K3Ts?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture\" allowfullscreen><\/iframe><\/p>\n<p><script>\n  (function(i,s,o,g,r,a,m){i['GoogleAnalyticsObject']=r;i[r]=i[r]||function(){\n  (i[r].q=i[r].q||[]).push(arguments)},i[r].l=1*new Date();a=s.createElement(o),\n  m=s.getElementsByTagName(o)[0];a.async=1;a.src=g;m.parentNode.insertBefore(a,m)\n  })(window,document,'script','https:\/\/www.google-analytics.com\/analytics.js','ga');<\/p>\n<p>  ga('create', 'UA-84644266-1', 'auto');\n  ga('send', 'pageview');<\/p>\n<p><\/script><\/p>\n","protected":false},"excerpt":{"rendered":"<p>DISC_gDNA_Generator Takes an RNA sequence as input to generate a list of DNA guides for DISC mediated cleavage covering the length of the RNA. Download gDNAgen_v1.1.exe You will need to have Python2.x installed. Double-click on the *.exe file. Select a<\/p>\n","protected":false},"author":6,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-749","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/pages\/749","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/users\/6"}],"replies":[{"embeddable":true,"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/comments?post=749"}],"version-history":[{"count":40,"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/pages\/749\/revisions"}],"predecessor-version":[{"id":1205,"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/pages\/749\/revisions\/1205"}],"wp:attachment":[{"href":"https:\/\/research.cbc.osu.edu\/musier-forsyth.1\/wp-json\/wp\/v2\/media?parent=749"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}