From zhuiastate.edu  Wed Mar 20 06:27:09 2013
From: "Hu, Zhiliang [AN S]" <zhuiastate.edu>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: FW: Construction of Genetic Map
Date: Wed, 20 Mar 2013 06:27:09 -0500

Jill,

You may have seen this post on ANGENMAP already. I forward it to this list
because I have heard that some recent SNP linkage experiments failed crimap
partly because of the large number of markers to handle. I know Dr Yang
from UMN is to tackle the problem with a de novo approach. Just wonder if
this is also on your targets?

Zhiliang

 
-----Original Message----- 
.From: rama bangera [mailto:rm_bangerayahoo.com] 
.Sent: Wednesday, March 20, 2013 6:03 AM 
.To: Multiple Recipients of 
.Subject: Construction of Genetic Map 

Dear all

I/we are working on QTL mapping in some traits in fish and have problems in
Preparing Genetic Map and/or recodingSNP's/preparing input files to use in
TMAP, OneMap, RQTL etc. Tried to prepare MAP using TMAP, RQTL, and OneMap
but with no success (just yet)

Background: The files I have in hand are, 1. genotype files for ~1400
candidates (half-sibs and full-sibs) including parents for about 10000
SNP's . SNPs are either AA, CC, GG, AG, CT.  A file with list of SNPs
.(This file is without header,animal id followed by SNPs in rows) 2. A file
with list of SNP's in rows ( in the order of above SNP) 3. Separate file
with Phenotypes

Questions:

1. We tried to run TMAP in windows (with proper input files) using Java. It
appeared to run but didnt give any output. Since I we dont find any proper
manual and/or troubleshoot information for TMAP, someone have any
suggestions? ( We tried with most of the Java Settings, with RAM
of 8Gb etc, but didnt work) 

2. For OneMap, the SNP location should be like for example: ac, ad, bc, a,
o, ab... etc. Any suggestions on how I can recode my SNP's (above) into
this format?

3. Is there any simple way/resource available to Recode SNP's and prepare
input files to use in different QTL softwares? 4. Any other suggestions :-)

Note: This work is part of my PhD thesis, I have been working with
Quantitative genetic data, but now also trying more of molecular/QTL
mapping and trying to improve

Many thanks in advance.

Rama Bangera PhD student at UMB Researcher at NOFIMA, Norway