{"id":16,"date":"2014-01-23T19:28:25","date_gmt":"2014-01-23T19:28:25","guid":{"rendered":"https:\/\/www.bio.cmu.edu\/labs\/mcmanus2\/?page_id=16"},"modified":"2025-03-12T17:45:13","modified_gmt":"2025-03-12T17:45:13","slug":"downloads","status":"publish","type":"page","link":"https:\/\/labs.bio.cmu.edu\/mcmanus\/downloads\/","title":{"rendered":"Software \/ Downloads"},"content":{"rendered":"<p><div class=\"et_pb_with_border et_d4_element et_pb_section et_pb_section_0 et_pb_with_background  et_pb_css_mix_blend_mode et_section_regular et_block_section\" >\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_d4_element et_pb_row et_pb_row_0  et_pb_css_mix_blend_mode et_block_row\">\n\t\t\t\t<div class=\"et_d4_element et_pb_column_4_4 et_pb_column et_pb_column_0  et_pb_css_mix_blend_mode et-last-child et_block_column\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_module et_d4_element et_pb_image et_pb_image_0\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<span class=\"et_pb_image_wrap \"><img loading=\"lazy\" decoding=\"async\" width=\"1779\" height=\"408\" src=\"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-content\/uploads\/sites\/2\/2025\/03\/cropped-logo5.gif\" alt=\"\" title=\"cropped-logo5.gif\" class=\"wp-image-462\" \/><\/span>\n\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div><div class=\"et_d4_element et_pb_section et_pb_section_1  et_pb_css_mix_blend_mode et_section_regular et_block_section\" >\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_d4_element et_pb_row et_pb_row_1  et_pb_css_mix_blend_mode et_block_row\">\n\t\t\t\t<div class=\"et_d4_element et_pb_column_4_4 et_pb_column et_pb_column_1  et_pb_css_mix_blend_mode et-last-child et_block_column\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_module et_d4_element et_pb_text et_pb_text_0  et_pb_text_align_left et_pb_bg_layout_light\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_text_inner\"><h4>Assemblies of the resequenced genomes of the Drosophila strains described in McManus, C.J., Coolon, J.D., Eipper-Mains, J., Wittkopp, P.J. and Graveley, B.R. (2014) Evolution of Splicing Regulatory networks in<i>Drosophila<\/i>.\u00a0<i>Genome Research<\/i>, in press.<\/h4><\/div>\n\t\t\t<\/div><div class=\"et_pb_module et_d4_element et_pb_text et_pb_text_1  et_pb_text_align_left et_pb_bg_layout_light\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_text_inner\"><p>The files included in this tar.gz contain the resequenced versions of the\u00a0<i>D. simulans<\/i>\u00a0(Tsimbazaza strain; Hollocher et al. 2000) and\u00a0<i>D. sechellia<\/i>\u00a0(Reference strain; 14021-0231.36) genomes, as well as genome from\u00a0<i>D. melanogaster<\/i>\u00a0strains zhr and z30 (McManus et al., 2014 (accepted)) in fasta format. Chain files are also included to convert coordinates on these genomes to those of the\u00a0<i>D. melanogaster<\/i>\u00a0reference version 3 (dm3), using the liftOver tool available on the UCSC genome browser website (http:\/\/hgdownload.soe.ucsc.edu\/admin\/exe\/). Custom perl scripts are also included to convert coordinates from the\u00a0<i>D. simulans<\/i>\u00a0and\u00a0<i>D. sechellia<\/i>\u00a0genomes into dm3 coordinates (as this is a multi-step process). You must have the liftOver tool installed in your path to use these perl scripts.<\/p><\/div>\n\t\t\t<\/div><div class=\"et_pb_button_module_wrapper et_pb_button_0_wrapper  et_pb_module \">\n\t\t\t\t<a class=\"et_pb_button et_d4_element et_pb_button_0 et_pb_bg_layout_light et_block_module\" href=\"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-content\/uploads\/sites\/2\/2018\/09\/SplicingRegDivGenomes.zip\" target=\"_blank\">Download Here<\/a>\n\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div><div class=\"et_d4_element et_pb_section et_pb_section_2  et_pb_css_mix_blend_mode et_section_regular et_block_section\" >\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_d4_element et_pb_row et_pb_row_2  et_pb_css_mix_blend_mode et_block_row\">\n\t\t\t\t<div class=\"et_d4_element et_pb_column_4_4 et_pb_column et_pb_column_2  et_pb_css_mix_blend_mode et-last-child et_block_column\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_module et_d4_element et_pb_text et_pb_text_2  et_pb_text_align_left et_pb_bg_layout_light\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_text_inner\"><h4>Mod-seeker data analysis pipeline for high-throughput probing of RNA chemical modification, as described in Talkish, J, May, GE, Lin, Y, Woolford JL, Jr, and McManus CJ. (2014).\u00a0Mod-seq: High-throughput sequencing for chemical probing of RNA structure.\u00a0<em>RNA<\/em> (accepted).<\/h4><\/div>\n\t\t\t<\/div><div class=\"et_pb_module et_d4_element et_pb_text et_pb_text_3  et_pb_text_align_left et_pb_bg_layout_light\">\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t<div class=\"et_pb_text_inner\"><p>The files included in this tar.gz contain mod-seeker analysis pipeline and test data.<\/p><\/div>\n\t\t\t<\/div><div class=\"et_pb_button_module_wrapper et_pb_button_1_wrapper  et_pb_module \">\n\t\t\t\t<a class=\"et_pb_button et_d4_element et_pb_button_1 et_pb_bg_layout_light et_block_module\" href=\"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-content\/uploads\/sites\/2\/2018\/09\/Mod-seeker.tar.gz\" target=\"_blank\">Download Here<\/a>\n\t\t\t<\/div>\n\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div>\n\t\t\t\t\n\t\t\t\t\n\t\t\t<\/div><\/p>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":21,"featured_media":0,"parent":0,"menu_order":6,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"<ol>\r\n<h4>Assemblies of the resequenced genomes of the Drosophila strains described in McManus, C.J., Coolon, J.D., Eipper-Mains, J., Wittkopp, P.J. and Graveley, B.R. (2014) Evolution of Splicing Regulatory networks in<i>Drosophila<\/i>.\u00a0<i>Genome Research<\/i>, in press.<\/h4>\r\nThe files included in this tar.gz contain the resequenced versions of the\u00a0<i>D. simulans<\/i>\u00a0(Tsimbazaza strain; Hollocher et al. 2000) and\u00a0<i>D. sechellia<\/i>\u00a0(Reference strain; 14021-0231.36) genomes, as well as genome from\u00a0<i>D. melanogaster<\/i>\u00a0strains zhr and z30 (McManus et al., 2014 (accepted)) in fasta format. Chain files are also included to convert coordinates on these genomes to those of the\u00a0<i>D. melanogaster<\/i>\u00a0reference version 3 (dm3), using the liftOver tool available on the UCSC genome browser website (http:\/\/hgdownload.soe.ucsc.edu\/admin\/exe\/). Custom perl scripts are also included to convert coordinates from the\u00a0<i>D. simulans<\/i>\u00a0and\u00a0<i>D. sechellia<\/i>\u00a0genomes into dm3 coordinates (as this is a multi-step process). You must have the liftOver tool installed in your path to use these perl scripts. (Download here -&gt;\u00a0<a href=\"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-content\/uploads\/sites\/2\/2018\/09\/SplicingRegDivGenomes.zip\">SplicingRegDivGenomes.zip<\/a>).\r\n<h4>Mod-seeker data analysis pipeline for high-throughput probing of RNA chemical modification, as described in Talkish, J, May, GE, Lin, Y, Woolford JL, Jr, and McManus CJ. (2014).\u00a0Mod-seq: High-throughput sequencing for chemical probing of RNA structure.\u00a0<em>RNA<\/em> (accepted).<\/h4>\r\nThe files included in this tar.gz contain mod-seeker analysis pipeline and test data\u00a0(Download here -&gt;<a href=\"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-content\/uploads\/sites\/2\/2018\/09\/Mod-seeker.tar.gz\">Mod-seeker.tar<\/a>\u00a0).\r\n\r\n\r\n&nbsp;&nbsp;&nbsp;&nbsp;\r\n&nbsp;&nbsp;&nbsp;&nbsp;\r\n&nbsp;&nbsp;&nbsp;&nbsp;","_et_gb_content_width":"","footnotes":""},"class_list":["post-16","page","type-page","status-publish","hentry"],"jetpack_sharing_enabled":true,"jetpack_shortlink":"https:\/\/wp.me\/ParKnc-g","_links":{"self":[{"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/pages\/16","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/users\/21"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/comments?post=16"}],"version-history":[{"count":9,"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/pages\/16\/revisions"}],"predecessor-version":[{"id":684,"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/pages\/16\/revisions\/684"}],"wp:attachment":[{"href":"https:\/\/labs.bio.cmu.edu\/mcmanus\/wp-json\/wp\/v2\/media?parent=16"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}