From GLicvm.tamu.edu  Wed Apr  3 09:23:27 2013
From: "Li, Gang" <GLicvm.tamu.edu>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: RE: General questions of using crimap
Date: Wed, 03 Apr 2013 09:23:27 -0500

Hi Zhiliang:
             Thank you very much for your reply. 
             I run crimap on a Linux server. This is a powerful machine which 
is assembled for De novo whole genome (human size ) sequences assembly of Next 
Generation sequencing data. RAM is big than 500G with 48 CPUs , system is 
OpenSuse Linux 11. But when I run crimap, even small data, it is still slow. 
The problem only can be set to run by one thread. I find a parallel crimap 
version on line , but the link of that one is invalid. Do you know any method 
to run crimap jobs using multiple threads? 
            Selection of subgroups (pedigree and markers) is based on the 
previous published works, like RH map and whole genome sequencing and 
assembly. The marker sequences have been blast to genome sequences and the 
given orders is used as an initial order to be checked.   Generations are 
mixed and kept in each subgroup. 
            Thanks of  the answer for the second question. I will try it 
today. 
Best regards, 
Gang 

-----Original Message----- 
.From: Hu, Zhiliang [AN S] [mailto:zhuiastate.edu] 
.Sent: Tuesday, April 02, 2013 10:40 PM 
.To: Multiple Recipients of 
.Subject: RE: General questions of using crimap 

 
Large SNP data for linkage analysis is known to be a computational
challenge lately. Do you wish to share the size of your computer (e.g. RAM,
CPU, OS, etc) and how you have selected your subgroups (e.g. pedigree,
number of 1st/2nd/etc generation individuals, number of markers, knowingly
from one chromosome or not, etc.)

For your second question, you may be interested in this example:
http://www.perlmonks.org/?node_id=839401

Zhiliang

-----Original Message----- 
.From: Li, Gang [mailto:GLicvm.tamu.edu] 
.Sent: Tuesday, April 02, 2013 10:18 PM 
.To: Multiple Recipients of 
.Subject: General questions of using crimap 

Hi Every One:
               I am a new user of crimap. 
               The data I have are 50,000 SNPs from a snp array provided by 
more than 300 individuals, it is a big matrix. Family structure are kind of 
complicate. Individual samples tested using this SNP array come from multiple 
families with complex structure. Original parents, parents and offspring are 
mixed together. 
                 1. Problems confused me now is the method to handle this 
data. After checking the literature, crimap is an appropriate  software to 
build the  linkage map using my data. But if I only used a partial data (with 
high informative markers), it is still very very slow to run everay thing, 
even twopoint. 
                 2. I try to separate the data to multiple subsets for each 
chromosome and use a sliding windows method to do a quick check of the 
published old maps. I can not run crimap in a batch model using a perl script, 
because of option 'prepare' requires several interrupt to ask users' options. 
Is there any way I can ignore that or let crimap automatically pick up 
options? 

Thank you so much for your any helps. Gang