{"id":37,"date":"2014-11-21T14:52:53","date_gmt":"2014-11-21T13:52:53","guid":{"rendered":"http:\/\/ist.blogs.inra.fr\/wdi\/?page_id=37"},"modified":"2018-11-12T16:36:55","modified_gmt":"2018-11-12T15:36:55","slug":"maps","status":"publish","type":"page","link":"https:\/\/ist.blogs.inrae.fr\/wdi\/maps\/","title":{"rendered":"Physical Maps"},"content":{"rendered":"<p>Physical maps are built using molecular biology techniques, like fingerprinting, to examine DNA molecules in order to show sequence features positions. Physical distance between landmarks is measured in base pairs.<\/p>\n<h2>Recommendations<\/h2>\n<h2 style=\"color: #ff0000\">Summary<\/h2>\n<h5 style=\"color: #ff0000\">To display physical maps in browsers performed by data managers:<\/h5>\n<ol>\n<li style=\"color: #ff0000\">Use the FPC format for physical map raw data<\/li>\n<li style=\"color: #ff0000\">Use the <a href=\"https:\/\/fairsharing.org\/FAIRsharing.dnk0f6\">GFF3<\/a> format for data integration<\/li>\n<\/ol>\n<p>&nbsp;<\/p>\n<h2 style=\"color: #26c4ec\">1. Raw data format and submission process<\/h2>\n<ul>\n<li style=\"list-style-type: none\">\n<ul>\n<li><strong>File formats<\/strong>:\u00a0We recommend using FPC file format (generate by FPC and LTC softwares).<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<ul>\n<li style=\"list-style-type: none\">\n<ul>\n<li><strong>Data submission<\/strong>:\u00a0INRA <a href=\"http:\/\/wheat-urgi.versailles.inra.fr\/\">URGI <\/a>is the official repository for <a href=\"http:\/\/www.wheatgenome.org\/\">IWGSC <\/a>physical maps. We recommend using the following submission support: <a href=\"http:\/\/wheat-urgi.versailles.inra.fr\/Seq-Repository\/Support-to-assembly-and-data-submission\">http:\/\/wheat-urgi.versailles.inra.fr\/Seq-Repository\/Support-to-assembly-and-data-submission<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<h2 style=\"color: #26c4ec\">2. Data integration file format<\/h2>\n<p>GFF3 is recommended to integrate data to feed GBrowse and display physical maps. Look at the &#8220;<a href=\"https:\/\/ist.blogs.inra.fr\/wdi\/genome-annotations\/\">Genome annotations<\/a>&#8221; recommendation part to find more details about GFF3 format. See also <a href=\"https:\/\/www.biostars.org\/p\/7615\/\" target=\"_blank\" rel=\"noopener\">how to produce GFF3<\/a>.<\/p>\n<h3 style=\"color: #ffa500\">Warning: GFF2 to GFF3 conversion<\/h3>\n<p>Converting a file from GFF2 to GFF3 format is problematic for several reasons. There are several GFF2 to GFF3 converters available on the web, but each makes specific assumptions about the GFF2 data that limit its applicability. GMOD does not endorse (or disparage) any particular converter. If you have GFF2 data from an external source, and they do not also provide it in GFF3 format, then you may be stuck with GFF2.<\/p>\n<p>If the GFF2 file does not use Sequence Ontology terms in column 3 then some sort of translation will need to be done on the types in the GFF2 to convert them to be SO terms.<\/p>\n<p>Another big problem is that GFF2 supports only one level of feature nesting. While you can certainly reproduce this minimal nesting in GFF3, it would be better to also convert your feature representations to be multi-level at the time you migrate the data to GFF3.<\/p>\n<p><strong>Convert data format<\/strong><br \/>\nYou can convert different formats to GFF3 using the <a href=\"https:\/\/bioconvert.readthedocs.io\/en\/master\/\">Bioconvert tool<\/a>.<\/p>\n<p><img loading=\"lazy\" decoding=\"async\" class=\"transparent\" src=\"https:\/\/bioconvert.readthedocs.io\/en\/master\/_images\/conversion.png\" alt=\"https:\/\/bioconvert.readthedocs.io\/en\/master\/_images\/conversion.png\" width=\"570\" height=\"389\" \/><\/p>\n<h2>Most popular tools<\/h2>\n<h2 style=\"color: #26c4ec\">Physical map building<\/h2>\n<ul>\n<li><a href=\"http:\/\/www.agcol.arizona.edu\/software\/fpc\/\">FPC software<\/a><\/li>\n<li><a href=\"http:\/\/www.biomedcentral.com\/1471-2105\/11\/584\">LTC software<\/a><\/li>\n<\/ul>\n<h2 style=\"color: #26c4ec\">Visualization tools<\/h2>\n<ul>\n<li style=\"list-style-type: none\">\n<ul>\n<li><a href=\"http:\/\/gmod.org\/wiki\/GBrowse\">GBrowse<\/a><\/li>\n<li><a href=\"http:\/\/jbrowse.org\/\">JBrowse<\/a><\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<h2><\/h2>\n<h2>Example<\/h2>\n<p>GFF3 sample of the <a href=\"https:\/\/urgi.versailles.inra.fr\/gb2\/gbrowse\/wheat_phys_pub\/\" target=\"_blank\" rel=\"noopener\">3B physical map browser<\/a>:<\/p>\n<pre>ctg110\tassembly\tcontig\t1\t1041601\t.\t.\t.\tSequence \"ctg110\"; Name \"ctg110\"\r\nctg110\tFPC\tBAC\t820801\t938401\t.\t.\t.\tBAC \"TaaCsp3BFhA_0290A06\"; Name \"TaaCsp3BFhA_0290A06\"; Contig_hit \"110\" \r\nctg110\tFPC\tBAC\t835201\t912001\t.\t.\t.\tBAC \"TaaCsp3BFhA_0130L06\"; Name \"TaaCsp3BFhA_0130L06\"; Contig_hit \"110\" \r\nctg110\tFPC\tBAC\t261601\t468001\t.\t.\t.\tBAC \"TaaCsp3BFhA_0117E07\"; Name \"TaaCsp3BFhA_0117E07\"; Contig_hit \"110\" \r\nctg110\tFPC\tBAC\t55201\t327601\t.\t.\t.\tBAC \"TaaCsp3BFhA_0111D21\"; Name \"TaaCsp3BFhA_0111D21\"; Contig_hit \"110\" \r\nctg110\u00a0\u00a0\u00a0 FPC\u00a0\u00a0\u00a0 marker\u00a0\u00a0\u00a0 808801\u00a0\u00a0\u00a0 808801\u00a0\u00a0\u00a0 .\u00a0\u00a0\u00a0 .\u00a0\u00a0\u00a0 .\u00a0\u00a0\u00a0 marker \"Ta#S32641420-3B\"; Name \"Ta#S32641420-3B\"; Contig_hit \"ctg110 - 1\" (TaaCsp3BFhA_0347M21) \r\nctg110\u00a0\u00a0\u00a0 FPC\u00a0\u00a0\u00a0 marker\u00a0\u00a0\u00a0 345601\u00a0\u00a0\u00a0 345601\u00a0\u00a0\u00a0 .\u00a0\u00a0\u00a0 .\u00a0\u00a0\u00a0 .\u00a0\u00a0\u00a0 marker \"Xcfp1207-3B\"; Name \"Xcfp1207-3B\"; Contig_hit \"ctg110 - 1\" (TaaCsp3BFhA_0017C12)<\/pre>\n<p>&nbsp;<\/p>\n<p>&nbsp;<\/p>\n<h2>Additional information<\/h2>\n<p><strong>Workflow for physical map data: <\/strong>click on the image<strong><br \/>\n<\/strong><a href=\"https:\/\/ist.blogs.inra.fr\/wdi\/wp-content\/uploads\/sites\/8\/2014\/11\/Workflow_phys_map.jpg\"><img loading=\"lazy\" decoding=\"async\" class=\" wp-image-277 alignnone\" src=\"https:\/\/ist.blogs.inra.fr\/wdi\/wp-content\/uploads\/sites\/8\/2014\/11\/Workflow_phys_map-300x225.jpg\" alt=\"Workflow_phys_map\" width=\"290\" height=\"218\" srcset=\"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-content\/uploads\/sites\/8\/2014\/11\/Workflow_phys_map-300x225.jpg 300w, https:\/\/ist.blogs.inrae.fr\/wdi\/wp-content\/uploads\/sites\/8\/2014\/11\/Workflow_phys_map.jpg 960w\" sizes=\"auto, (max-width: 290px) 100vw, 290px\" \/><\/a><\/p>\n<p>&nbsp;<\/p>\n<p><span style=\"color: #33aabd\">Written on:<\/span>\u00a0WDI working group<br \/>\n<span style=\"color: #33aabd\">Published on:<\/span> 02 October 2014<br \/>\n<span style=\"color: #33aabd\">Updated on:<\/span>\u00a009\u00a0July\u00a02015<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Physical maps are built using molecular biology techniques, like fingerprinting, to examine DNA molecules in order to show sequence features positions. Physical distance between landmarks is measured in base pairs. Recommendations Summary To display physical maps in browsers performed by data managers: Use the FPC format for physical map raw data Use the GFF3 format [&hellip;]<\/p>\n","protected":false},"author":11,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-37","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/37","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/comments?post=37"}],"version-history":[{"count":0,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/37\/revisions"}],"wp:attachment":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/media?parent=37"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}