{"action":"opened","issue":{"url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/issues/78","labels_url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/issues/78/labels{/name}","comments_url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/issues/78/comments","events_url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/issues/78/events","html_url":"https://github.com/TeselaGen/Peony-Issue-Tracking/issues/78","id":115540742,"number":78,"title":"Sequencing Primer Design utility for generating sequencing primers","user":{"login":"craftjk","id":4167907,"avatar_url":"https://avatars.githubusercontent.com/u/4167907?v=3","gravatar_id":"","url":"https://api.github.com/users/craftjk","html_url":"https://github.com/craftjk","followers_url":"https://api.github.com/users/craftjk/followers","following_url":"https://api.github.com/users/craftjk/following{/other_user}","gists_url":"https://api.github.com/users/craftjk/gists{/gist_id}","starred_url":"https://api.github.com/users/craftjk/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/craftjk/subscriptions","organizations_url":"https://api.github.com/users/craftjk/orgs","repos_url":"https://api.github.com/users/craftjk/repos","events_url":"https://api.github.com/users/craftjk/events{/privacy}","received_events_url":"https://api.github.com/users/craftjk/received_events","type":"User","site_admin":false},"labels":[{"url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/labels/Customer:%20DAS%20Phase%20I","name":"Customer: DAS Phase I","color":"e11d21"},{"url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/labels/Priority:%20Low","name":"Priority: Low","color":"FFFF57"},{"url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/labels/Priority:%20Medium","name":"Priority: Medium","color":"F39C12"},{"url":"https://api.github.com/repos/TeselaGen/Peony-Issue-Tracking/labels/Type:%20Feature","name":"Type: Feature","color":"8B2E5F"}],"state":"open","locked":false,"assignee":null,"milestone":null,"comments":0,"created_at":"2015-11-06T16:34:59Z","updated_at":"2015-11-06T16:34:59Z","closed_at":null,"body":"_From @sampearl on August 21, 2015 0:1_\n\n* Supporting Materials:\r\n  * [Sequencing PPT](https://drive.google.com/open?id=0B_l-WxHozfYhS1lKSlpRTEZPWGM) from Scott Bevan\r\n  * [Primer Design scripts](https://drive.google.com/file/d/0B_l-WxHozfYhdm11em5iclFWdGc/view?usp=drive_web) by Hank Wu via Bill Moskal \r\n* Goal: primers that are spaced at regular intervals to generate data for a large piece of DNA\r\n* Need to design primers on both strands of the DNA\r\n* Existing tools: Primer3 (also used by j5)\r\n* Steps (from Vector NTI):\r\n  * Select the portion of the sequence for which you would like to design primers\r\n  * Specify a window size (ideal spacing between primers)\r\n  * Specify parameters (length, GC content, etc.) – normally use the same parameters every time \r\n  * Specify the strand – would be nice to do either strand or both strands at once\r\n  * Specify the number of primers per window – we almost always want one primer\r\n  * Click okay (primers are designed)\r\n  * Name the primers and save them to your database (very poorly implemented in VNTI)\r\n  * Examine the sequence immediately adjacent to (upstream of) each window\r\n  * If this sequence matches the parameters set by the user, it becomes a primer\r\n  * If the sequence doesn’t match the parameters, move one base pair at a time until a sequence that matches the parameter is found\r\n  * Scott would prefer to look inside the window rather than outside “(this is a “next level” need)”\r\n  * Scott would “really prefer a checkbox to select either strategy”\r\n* If you have a set of combinatorially created plasmids, you can use the same primers to sequence multiple plasmids → Two workflows:\r\n  * Low/medium throughput:\r\n    * Primers are expensive ($4.50 each)\r\n    * Must re-use existing primers to be cost efficient\r\n    * When sequencing a new plasmid, we need a tool to identify suitable existing primers and to fill gaps with new primer synthesis\r\n  * High throughput\r\n    * Primers are cheap at bulk pricing ($1.40)\r\n    * Use a primer once and throw it away\r\n    * Design a new set of primers for the next plasmid (primer reuse is a non issue)\r\n    * LIMS capabilities need to be enhanced to keep track of primers/sequences etc (Phase II?) Currently using RCC/Penelope/Olaf\r\n    * RefID/sequences/PCRproducts/Clones/PCRscreen/Sequence/Primers/ → genoread validated targets move one, others must be reworked.\r\n    * Currently using [Primer Design scripts](https://drive.google.com/file/d/0B_l-WxHozfYhdm11em5iclFWdGc/view?usp=drive_web) by Hank Wu via Bill Moskal\r\n  * Note ‘Difficulties in Reusing Primers’ in the [PPT from Scott Bevan](https://drive.google.com/open?id=0B_l-WxHozfYhS1lKSlpRTEZPWGM)\r\n* Contact: Scott Bevan, David Mann\n\n_Copied from original issue: TeselaGen/ve#1269_"}}