1. Select all loci in map order on chromosome: ##
  2. Select by locus number.
  3. Select one chromosome and select loci on it.
  4. Select one or more chromosomes and select loci on them.
  5. HINTS

V - The locus reordering menu

The locus reordering menu allows the user to reorder the loci into the map order as specified in the map file, or into a user-chosen order. The user can also select subsets of loci from a list of loci.

LOCUS REORDERING MENU
 1) Select all loci in map order on chromosome: 5
 2) Select by locus number.
 3) Select one chromosome and select loci on it.
 4) Select one or more chromosomes and select loci on them.


1) Select all loci in map order on chromosome: ##

Option 1 selects all loci for a specified chromosome, rearranging them into map order as specified by the input map file. It will also place all trait loci before the ordered markers.

2) Select by locus number.

Option 2 permits the user to select a set of loci from a numbered list by entering their numbers in the desired order. The user may at any time during the selection process type in the character ‘v’ to review the original loci list or ‘o’ to view all the loci he/she has selected. To finalize the selection process the user will include an ‘e’ at the end of the string or on the next input line (e.g. ‘1 3 8-11 e’ is a typical input string and will select the loci at the 1, 3, 8 through 11th positions in the original locus order).
HINT: Several of the output options will complain if markers are not ordered according to their map positions, so this has to be kept track of while re-ordering the loci manually.

3) Select one chromosome and select loci on it.

Option 3 will permit only loci from the user-specified chromosome to be retrieved into a new loci set. The user may then select all the loci for that chromosome or may select a subset of these loci. If the input data files contain markers from more than one chromosome, then the user may also select another chromosome as the chromosome to be used in generating the output files.

4) Select one or more chromosomes and select loci on them.

Option 4 is used to set up multiple sets of files, one for each chromosome. When Option 4 is chosen, this submenu appears:

 1) Select all marker loci on all chromosomes. 
 2) Select marker loci on specific chromosomes.


HINTS

Re: Sub-Option 1 ‘Select all markers in order on all chromosomes with trait locus first’:
A) If you wish to create a set of LINKAGE-format files with all the markers re-arranged into their map order, one chromosome after the other, choose Option ‘18) Convert to Linkage-format’ from the Analysis menu and then choose the sub-option 1 ‘Select all markers in order on all chromosomes from Option 4 of the Locus Reordering Menu. This is useful, for example, if you want to run the Analyze package and you want all the markers in chromosomal order.
B) If you have a single affection status locus in your input files, and then choose sub-option 1 from Option 4 of the Locus Reordering Menu, then Mega2 will create multiple sets of chromosome-specific files for many of the analysis options, including ASPEX, GeneHunter-Plus, and GeneHunter. A ‘global’ C-shell script will be created that will analyze one chromosome after another, all at once. This greatly eases analyses of genome-wide data sets.