{"id":2032,"date":"2016-10-31T21:33:50","date_gmt":"2016-10-31T21:33:50","guid":{"rendered":"http:\/\/www.jmhartley.com\/HBlog\/?p=2032"},"modified":"2017-04-13T11:36:02","modified_gmt":"2017-04-13T11:36:02","slug":"dna-phasing-of-raw-dna-when-one-sibling-is-missing-part-10","status":"publish","type":"post","link":"http:\/\/www.jmhartley.com\/HBlog\/2016\/10\/31\/dna-phasing-of-raw-dna-when-one-sibling-is-missing-part-10\/","title":{"rendered":"DNA Phasing of Raw DNA When One Sibling is Missing: Part 10"},"content":{"rendered":"<p>In this Blog, I would like to portray my phasing results in an Excel Bar Chart if possible. This has been one of the most difficult parts a phasing my DNA for me.<\/p>\n<p>I have looked at Stacked Bar Charts in Excel as they seem to be the closest to what I am looking for. Today I looked at a method for producing Gantt Charts at ablebits.com which seems to hold some promise of application for DNA mapping:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/bar-chart-excel.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2033\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/bar-chart-excel.png\" alt=\"bar-chart-excel\" width=\"626\" height=\"376\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/bar-chart-excel.png 626w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/bar-chart-excel-300x180.png 300w\" sizes=\"(max-width: 626px) 100vw, 626px\" \/><\/a><\/p>\n<p>I had my Maternal Patterns&#8217; Starts and Stops from <a href=\"http:\/\/www.jmhartley.com\/HBlog\/?p=1995\">my last blog<\/a>. I took those and converted them to Build 36 and put them in a spreadsheet:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MomCrossoversTable.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2034\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MomCrossoversTable.png\" alt=\"momcrossoverstable\" width=\"710\" height=\"268\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MomCrossoversTable.png 710w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MomCrossoversTable-300x113.png 300w\" sizes=\"(max-width: 710px) 100vw, 710px\" \/><\/a><\/p>\n<p>Start is the ID# I was using. Start36 is the Chromosome position of the Start of the pattern in Build 36. App ID is the approximate position of the Crossover. Then I have that same location in Build 37 and Build 36. Following the logic in the Ablebits.com tutorial, I have the first Maternal Crossovers for Chromosome 7 in my simplified Chart:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MatFirstXOver7.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2035\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MatFirstXOver7.png\" alt=\"matfirstxover7\" width=\"497\" height=\"404\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MatFirstXOver7.png 497w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/MatFirstXOver7-300x244.png 300w\" sizes=\"(max-width: 497px) 100vw, 497px\" \/><\/a><\/p>\n<p>I got this by choosing the Build 36 column and choosing Insert Stacked Bar. I suppose a better Title would have been Chromosome 7 Maternal Crossover rather than Build 36. This was taken from my Column Header. The goal is to get a 2 color bar above. However, I already see a problem. The bar needs to be different colors for different people. Well, I have to start somewhere.<\/p>\n<p>Next, I put in the next crossover location for each person. I took this position and subtracted from it the first Crossover to get a length.<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Step2CrossExcel.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2036\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Step2CrossExcel.png\" alt=\"step2crossexcel\" width=\"579\" height=\"395\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Step2CrossExcel.png 579w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Step2CrossExcel-300x205.png 300w\" sizes=\"(max-width: 579px) 100vw, 579px\" \/><\/a><\/p>\n<p>You may note that the Bar Chart inverts the original order. It gives Sharon a 4 which is now on top. Here is my visual phasing of Chromosome 7 that I am trying to replicate:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7VisPhase.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2037\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7VisPhase.png\" alt=\"chr7visphase\" width=\"640\" height=\"222\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7VisPhase.png 640w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7VisPhase-300x104.png 300w\" sizes=\"(max-width: 640px) 100vw, 640px\" \/><\/a><\/p>\n<p>My Excel Bar Chart order is Sharon, Jon, Joel, Heidi. My visual phasing order is Sharon, Joel, Heidi, Jon. The 2 maternal colors I have above are green and orange representing Lentz and Rathfelder. If I keep orange as Rathfelder, that means I want to change bar 2 and 3 (Joel and Jon) on the Excel Bar Chart. One way to do this is to move over the first Crossovers for Joel and Jon in my spreadsheet:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/ModChart.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2038\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/ModChart.png\" alt=\"modchart\" width=\"597\" height=\"416\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/ModChart.png 597w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/ModChart-300x209.png 300w\" sizes=\"(max-width: 597px) 100vw, 597px\" \/><\/a><\/p>\n<p>However, that made the 2 male siblings&#8217; first maternal grandparent match too long. I needed to move the start over 2 places in my spreadsheet:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Mat7Revised.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2039\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Mat7Revised.png\" alt=\"mat7revised\" width=\"591\" height=\"410\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Mat7Revised.png 591w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Mat7Revised-300x208.png 300w\" sizes=\"(max-width: 591px) 100vw, 591px\" \/><\/a><\/p>\n<p>Now the\u00a0Chr7 Maternal Crossover column can be called Lentz and the 2length column can be called Rathfelder.<\/p>\n<p>Next, I added another column for the next Lentz portion of DNA:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr73rdXover.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2040\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr73rdXover.png\" alt=\"chr73rdxover\" width=\"706\" height=\"427\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr73rdXover.png 706w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr73rdXover-300x181.png 300w\" sizes=\"(max-width: 706px) 100vw, 706px\" \/><\/a><\/p>\n<p>I was hoping that if I named the next column Lentz, that Excel would give me the same blue as the first Lentz. I was able to right click on the gray and change it to blue. I then added another Rathfelder segment. For this to work in Excel, a Rathfelder length is added rather than a start and stop location.<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/cHR7Xover3.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2041\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/cHR7Xover3.png\" alt=\"chr7xover3\" width=\"791\" height=\"412\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/cHR7Xover3.png 791w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/cHR7Xover3-300x156.png 300w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/cHR7Xover3-768x400.png 768w\" sizes=\"(max-width: 767px) 89vw, (max-width: 1000px) 54vw, (max-width: 1071px) 543px, 580px\" \/><\/a><\/p>\n<p>Again, I had to reformat the Excel-chosen color to be consistent with what I had for Rathfelder. I chose the last position for Heidi and Sharon as the highest that I had as this was their last segment. After a bit of wrangling with Excel, I was able to get this:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2042\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7.png\" alt=\"chr7\" width=\"908\" height=\"406\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7.png 908w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7-300x134.png 300w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7-768x343.png 768w\" sizes=\"(max-width: 767px) 89vw, (max-width: 1000px) 54vw, (max-width: 1071px) 543px, 580px\" \/><\/a><\/p>\n<p>So that is the presentation. However, I notice that on my visual phasing, I had 5 segments for Jon and only 4 here. I missed his last Rathfelder segment. I had ended Jon&#8217;s Chromosome too early. Here is the correction:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7corrected.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2043\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7corrected.png\" alt=\"chr7corrected\" width=\"872\" height=\"460\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7corrected.png 872w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7corrected-300x158.png 300w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7corrected-768x405.png 768w\" sizes=\"(max-width: 767px) 89vw, (max-width: 1000px) 54vw, (max-width: 1071px) 543px, 580px\" \/><\/a><\/p>\n<p>It still looks like one of Jon&#8217;s crossovers in the middle of the Chromosome may be off, but I&#8217;ll have to figure that out later.<\/p>\n<h4>Paternal Bar Chart<\/h4>\n<p>Now that I have something that looks like a maternal Chromosome Map, I need the paternal side to go along with it. It looks like if I add 4 more rows to my spreadsheet, I may have it.<\/p>\n<p>I did this and I added Hartley and Frazer (my paternal side grandparents) to the right of the maternal side grandparents. I had to make a new chart that came out like this:<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7MatPat.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2045\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7MatPat.png\" alt=\"chr7matpat\" width=\"724\" height=\"477\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7MatPat.png 724w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7MatPat-300x198.png 300w\" sizes=\"(max-width: 724px) 100vw, 724px\" \/><\/a><\/p>\n<p>Here #4 is my Paternal DNA. I found it a bit disconcerting that my paternal side was longer than the maternal. Here I&#8217;ve added a bit of formatting and made the colors consistent (one color per grandparent):<\/p>\n<p><a href=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7PatMatMap.png\"><img loading=\"lazy\" decoding=\"async\" class=\"alignnone size-full wp-image-2046\" src=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7PatMatMap.png\" alt=\"chr7patmatmap\" width=\"747\" height=\"433\" srcset=\"http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7PatMatMap.png 747w, http:\/\/www.jmhartley.com\/HBlog\/wp-content\/uploads\/2016\/10\/Chr7PatMatMap-300x174.png 300w\" sizes=\"(max-width: 706px) 89vw, (max-width: 767px) 82vw, 740px\" \/><\/a><\/p>\n<p>Well, I guess I&#8217;ll just leave this imperfect. It will give me something to work on later. I did change the scale from millions to M&#8217;s to be easier to read. \u00a0The above shows that Jon and Heidi share their paternal grandfather&#8217;s Hartley DNA un-recombined on Chromosome 7.<\/p>\n<h4>Summary and Conclusions<\/h4>\n<ul>\n<li>Learning how to phase my raw DNA has been interesting and time consuming<\/li>\n<li>Delving into the A&#8217;s, G&#8217;s, T&#8217;s and C&#8217;s promotes understanding of one&#8217;s DNA<\/li>\n<li>I owe a lot to M MacNeill and Whit Athey in learning how to do this phasing<\/li>\n<li>Due to the data intensive nature of phasing, I would recommend the use of MS Access or some other database software.<\/li>\n<li>An understanding of Excel or similar spreadsheet software is also important.<\/li>\n<li>I had tested my brother Jon as an afterthought. It turned out that his test results were important in determining the phasing of the 4 siblings.<\/li>\n<li>I have the overall skeleton of the phasing with crossovers. There is still a lot of work to complete the individual Chromosomes and trouble shoot problem areas.<\/li>\n<li>Further, I have not worked on the X Chromosome due to the different nature of that Chromosome. My brother and I are already phased. My sisters are not.<\/li>\n<li>Once these maps are done they will be a reference to all matches to my 3 siblings and myself.<\/li>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>In this Blog, I would like to portray my phasing results in an Excel Bar Chart if possible. This has been one of the most difficult parts a phasing my DNA for me. I have looked at Stacked Bar Charts in Excel as they seem to be the closest to what I am looking for. &hellip; <\/p>\n<p class=\"link-more\"><a href=\"http:\/\/www.jmhartley.com\/HBlog\/2016\/10\/31\/dna-phasing-of-raw-dna-when-one-sibling-is-missing-part-10\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;DNA Phasing of Raw DNA When One Sibling is Missing: Part 10&#8221;<\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[11,23,37],"tags":[],"_links":{"self":[{"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/posts\/2032"}],"collection":[{"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/comments?post=2032"}],"version-history":[{"count":3,"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/posts\/2032\/revisions"}],"predecessor-version":[{"id":2048,"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/posts\/2032\/revisions\/2048"}],"wp:attachment":[{"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/media?parent=2032"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/categories?post=2032"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.jmhartley.com\/HBlog\/wp-json\/wp\/v2\/tags?post=2032"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}