From jillian.maddoxalumni.unimelb.edu.au  Sun Feb 23 22:04:57 2014
From: Jill Maddox <jillian.maddoxalumni.unimelb.edu.au>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: RE: When to stop flipping?
Date: Sun, 23 Feb 2014 22:04:57 -0600

Hi All

My 2c re flipping. The appropriate flips number etc depends how dense a map
is. flips2 is only useful for very low density maps and is unsuitable for
high density linkage maps. Whilst higher numbers of flips are slower they
consider orders not considered by the flips2 approach, and one doesn't have
to run from as many different start
orders (i.e. less manual input - I found starting off with lower  
flips numbers led to me spending more time rejigging starting orders  
than using a higher flips number). 

I try for the highest flips number I can get to run within a reasonable
timeframe (hopefully less than a month although less than a week is nicer),
and I have often tried flips7 for smaller chromosomes. One option is to use
the command line switch option that allows one to specify different start
and finish loci so that one can run multiple flips jobs for different
regions of the same chromosome simultaneously. zero or more of:
  -s start_locus_number [1..num_loci] 
  -S start_locus_name 
  -e end_locus_number    (for flips) 
  -E end_locus_name 
Examples: 
crimap 1 flips7 -s 158 -e 8 
crimap 1 flips7 -S DU214400 -e KAP8 

If starting from a physical order that is purely derived from assembly of
sequence without other information then it may be better to remove less
informative markers (fewer informative meioses) from the data set so that
you can test a framework of the more highly informative markers with
flipping to check that there are no gross
ordering differences between the physical and linkage maps. You can  
then add the less informative markers back in to their best physical  
positions and check with flipping. 

Ideally the flips part of CRI-MAP should be parallelised to take advantage
of as many cpu's as are available in modern systems - it was on our to-do
list but needs funding - Ian and I are still working
on an alternate way to build faster de novo maps. 

Regards

 
Jill 
At 02:12 PM 24/02/2014, Hu, Zhiliang [AN S] wrote: 

>
>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 
> 
>