Editing
Chris:LabNotes/FateMapping/Calendar/2015/2015-5-23
(section)
Jump to navigation
Jump to search
Warning:
You are not logged in. Your IP address will be publicly visible if you make any edits. If you
log in
or
create an account
, your edits will be attributed to your username, along with other benefits.
Anti-spam check. Do
not
fill this in!
===New 20150523 probe design=== *We now wanted to design a new set of probes for an expected set of targets. These probes will be designed using a modified version of ppDesigner that allows for finer tuning of the capture arm melting temperatures. Previously, the melting temperatures were set with global parameters $primerMaxTm/$primerMinTm in the probe_parameters.pl file. It would result in probes that had ligation/extension arms that were generally between the melting temperatures of 55/65C. *However, Dr. Zhang noticed that the best probe captures happened when the ligation arm melting temperatures were higher (along with extension arm Tm being ~5C lower than ligation arm Tm). Consequently, we want to edit ppDesigner in order to set the melting temperature of ligation arms to anywhere between 66 and 72. Then, we want to control the melting tmeperature of the extension arms to be within 4-8C of the ligation arm Tm. This was all done by editing the get_probes.pl script within ppDesigner. The final ppDesigner zipped program is found in [[File:cw_20150523_ppDesigner_BSPP_v2.0_edit.zip]] **Note:Because we had to increase the melting temperature of the probes, I also increased the total length of the two capture arms H1_plus_H2_len to 48 from 42bp in the jobFile. *The final ppDesigner run was in genome-miner </home/cjwei/Fate_Mapping/pp_design/ppDesigner_20150523/>. *We then wanted to filter by alignment and alignability using the same procedure as <http://genome-tech.ucsd.edu/LabNotes/index.php/Chris:LabNotes/FateMapping/Calendar/2014/2014-9-22> and then wanted to '''only choose the probes that were not also covered by the cherry-picked 20140922 probes.''' This was all done in genemapster at </media/3TB_slot2/cjwei/Fate_Mapping/pp_design/ppDesigner_20150523>
Summary:
Please note that all contributions to ZhangLabWiki may be edited, altered, or removed by other contributors. If you do not want your writing to be edited mercilessly, then do not submit it here.
You are also promising us that you wrote this yourself, or copied it from a public domain or similar free resource (see
ZhangLabWiki:Copyrights
for details).
Do not submit copyrighted work without permission!
Cancel
Editing help
(opens in new window)
Navigation menu
Personal tools
Not logged in
Talk
Contributions
Create account
Log in
Namespaces
Page
Discussion
English
Views
Read
Edit
View history
More
Search
Navigation
Main Page
Current events
Recent changes
Random page
Investigators
Matt Cai
Song Chen
Eric Chu
Dinh Diep
Elizabeth Duong
Shicheng Guo
Alan Fung
Daniel Jacobsen
Blue Lake
Huy Lam
Alice Li
Andrew Richards
Brandon Sos
Chris Wei
Yan Wu
Kun Zhang
Tools
What links here
Related changes
Special pages
Page information