From GLicvm.tamu.edu  Thu Apr  4 09:49:45 2013
From: "Li, Gang" <GLicvm.tamu.edu>
To: Multiple Recipients of <crimap-usersanimalgenome.org>
Subject: RE: General questions of using crimap
Date: Thu, 04 Apr 2013 09:49:45 -0500

Hi Jill:
     Thank you very much.   This problem have been resolved. 
     Because my data is a big matrix, more than 50,000 markers. It is still 
take long time to run twopoint calculation.  I notice only one thread is using 
for crimap running. Do you have any suggestion to run crimap applying multiple 
thread? 
     I appreciate your help. 
Best regards, 
Gang 

 

 
-----Original Message----- 
.From: Jill Maddox [mailto:jillian.maddoxalumni.unimelb.edu.au] 
.Sent: Wednesday, April 03, 2013 6:55 PM 
.To: Li, Gang; Multiple Recipients of 
.Subject: Re: General questions of using crimap 

Hi Gang

There are 2 ways to run prepare without having to do keyboard input.

The first is to just use lispcri rather than crimap to run prepare. If you
don't specify otherwise lispcri is built automatically when CRI-MAP is made
- just make sure it is in your path. If it hasn't been built then do make
lispcri in the source code directory. e.g. lispcri n prepare > chrn.prepare
where n is the number of your chromosome Make sure that there is not
already a chrn.dat file in the directory as if there is then lispcri will
hang.

The second way is to create an answer file for crimap with the answers that
you want to use. e.g. input file called ans containing the following lines
N N N N 8 Y

replace the 8 with whichever CRI-MAP option you want to do then invoke with
crimap n prepare chrn.prepare Note that the same caveat re pre-existing dat
files applies. If there is a pre-existing dat file either delete it or set
up a slightly different answer file to allow for it so that the answers in
the file match the questions asked.

Regards

 
Jill 
At 02:17 PM 3/04/2013, Li, Gang wrote: 

>
>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 
> 
> 
>~~>bioinfo-teamanimalgenome.org>Program - Supported by USDA/NIFA>crimap-users-requestanimalgenome.org 

 
*************************************************************** 

Jill Maddox 16 Park Square Port Melbourne, 3207 Australia phone: 03 9646
0428 E-mail: jillian.maddoxalumni.unimelb.edu.au

***************************************************************