From zhuiastate.edu  Sun Feb 23 21:12:39 2014
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: RE: When to stop flipping?
Date: Sun, 23 Feb 2014 21:12:39 -0600

Jisca,

You may wish to take a look at this scroll-through tutorial to start with:
http://www.animalgenome.org/hu/CRIMAPwkshp/  (step 6). In general you'd like to
make the sum LODs smaller by flipping - when this come to little changes
after a flip, it implies an optimal order is close.

Flips2 is my good friend. Multiple flips at a time is slower, often used in
the beginning to quickly settle with a rough order before you do flips2.

You will learn once you start. Have fun and good luck,

Zhiliang

 
-----Original Message----- 
.From: Jisca Huisman [mailto:jisca.huismaned.ac.uk] 
.Sent: Sunday, February 23, 2014 10:54 AM 
.To: Multiple Recipients of 
.Subject: When to stop flipping? 

Dear all,

Could anyone please advice me on when to stop doing flips, based on their
experience or guidelines? We have a reasonably good idea of the
order of our SNPs based on a related species, but besides some known 
major rearrangements most likely many minor rearrangements have occurred. 

Within each round of flips, which threshold to use to try and flip? So far
we have rather arbitrarily used a relative log likelihood of -0.5, but I
would like to know where the threshold lies between exploring enough
alternative maps, versus the risk of creating 'false positives'. Sometimes
after making one flip with a low relative logL (e.g. -0.6), several other
flips with much higher relative logL are suggested (e.g. -4 or -5). Using a
fixed threshold would be helpful, both in terms of reproducibility and to
automate the process.

Additionally, is there a way to predict if flips(n+1) is worth doing? For
example, if flips3 gives little improvement in logLikelihood, is it
worthwhile to do the much slower flips4? And how many 'alternative
scenarios' should one consider, where one starts of with a different
initial set of flips?

Thank you,

Jisca Huisman, Postdoctoral researcher Wild Evolutionary Genetics group
Institute of Evolutionary Biology University of Edinburgh