作图软件的操作.ppt

第11讲 植物QTL作图软件的操作 units cm cent func kossambi make chrom chrom1 chrom2 chrom3 seq 1 anchor chrom1 seq 4 anchor chrom2 seq 13 anchor chrom3 error det on seq all error prob 0.5 two point save 1.3 mapmaker/exe 3.0操作流程 # 画出染色体图谱 Using MAPMAKER/EXP You will need Mapmaker/EXP for this part. If you dont want to use Mapmaker/EXP, then you can use the already prepared files that come with the distribution. Otherwise, ftp to and cd to distribution/mapmaker to get the programs. A file sample.raw comes with Mapmaker/EXP. Each number is a command in a sequence to be done in Mapmaker/EXP. Anything inside of square braces are comments and should not be typed into Mapmaker/EXP. Start up Mapmaker/EXP in an appropriate subdirectory and proceed with these commands: prepare data sample.raw [Input the data from the raw file.] photo sample.tutorial [Save what you do in a log file.] sequence 1 2 3 4 5 6 7 8 9 10 11 12 [Start with all markers.] group [Group them into linkage groups] sequence { 1 2 3 5 7 } [Use randomly ordered group 1 makers.] compare [Compare all orders. For each in turn, calculate the Likelihood.] sequence 1 3 2 5 7 [Decide that this is the best order and specify it.] map [Print the map to the screen. This attaches distances as well.] sequence 4 6 8 9 10 11 12 [Now use the rest of the markers.] list loci [Summarize the number of informative progeny.] lod table [Show pairwise distances and linkage LOD scores.] sequence {8 9 10 11 12} [Use a randomly ordered subset of markers from group 2.] compare [Compare all orders. For each in turn, calculate the Likelihood.] sequence order1 [Use the best order from the compare command.] try 4 6 [Try all possible positions of markers 4 and 6. Also, try unlinked idea.] sequence 4 11 8 12 9 6 10 [This is the best sequence.] make chromosome c1 [Create chromosome 1.] sequence 1 3 2 5 7 [Specify the sequence of markers on chromosome 1.] attach c1 [Attach the seque