作圖軟件的操作

1、第第11講講 植物植物QTL作圖軟件的操作作圖軟件的操作1. MAPMAKER/EXP 3.01.1 安裝和運行安裝和運行 復(fù)制復(fù)制MAPMAKER文件夾到文件夾到C盤盤 解壓解壓MAPM3PC1.EXE和和MAPM3PC2.EXE壓縮包壓縮包 雙擊程序雙擊程序mapmaker.bat 1.2 數(shù)據(jù)文件準備數(shù)據(jù)文件準備源文件（源文件（*.raw）群體：回交群體、群體：回交群體、F2群體、群體、F3群體、群體、RIL群體以及群體以及DH群群體體格式data type f2 intercross20 5 2 #Joes tiny data set,10/21 version.*locus1 BBB

2、HH-AAABBBHHH-AABA*locus2 AB-ABHABHAB-ABHABHBH*locus3 ABBAHHHBHABHABHBBHH-*locus4 ABHABAAAHAB-ABHABHHB*locus5 ABHABHAA-ABHABHAHHHB*Trait1 6.3 7.7 8.0 6.2 8.8 6.2 4.1 6.5 5.4 7.3 8.7 9.0 5.2 6.8 7.2 7.1 7.6 8.3 8.1 7.5*Trait2 5.5 5.5 5.5 4.5 4.5 4.5 3.5 3.5 3.5 5.5 5.5 4.5 4.5 4.5 3.5 5.2 6.8 7.2 7.1群

3、體群體類型類型個體數(shù)、個體數(shù)、標記數(shù)和標記數(shù)和性狀數(shù)性狀數(shù)# 注注釋釋* 標記標記* 性狀性狀 data type f2 intercross20 5 2 symbols 1=A 3=B 2=H 0=-#Joes tiny data set,10/21 version.*locus1 3 3 3 2 2 0 1 1 3 3 3 2 2 2 1 1 3 1*locus2*locus3*locus4 *locus5*Trait1 6.3 7.7 8.0 6.2 8.8 6.2 4.1 6.5 5.4 7.3 8.7 9.0 5.2 6.8 7.2 7.1 7.6 8.3 8.1 7.5*Trait

4、2 5.5 5.5 5.5 4.5 4.5 4.5 3.5 3.5 3.5 5.5 5.5 4.5 4.5 4.5 3.5 5.2 6.8 7.2 7.11.2 數(shù)據(jù)文件準備數(shù)據(jù)文件準備1. 源文件（源文件（*.raw）*.data，*.map，*.tra*.2pt，*.3pt，*.qtl2. 源文件的中間文件源文件的中間文件1 prep data *.raw*.raw2 load data *.raw1.2 數(shù)據(jù)文件準備數(shù)據(jù)文件準備 3. 初始化文件初始化文件1 prep data *.raw*.pre# 定義染色體的數(shù)量和名稱定義染色體的數(shù)量和名稱# 錙定標記，指定染色體所屬的連鎖群錙定標

5、記，指定染色體所屬的連鎖群# 進行兩點測驗，為進一步分析提供信息等進行兩點測驗，為進一步分析提供信息等1.2 數(shù)據(jù)文件準備數(shù)據(jù)文件準備 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*.pre file1.3 mapmaker/exe 3.0操作流程操作流程1.3.1 簡單圖譜的制作簡單圖譜的制作1pr

6、epare data sample.raw# 調(diào)用數(shù)據(jù)文件調(diào)用數(shù)據(jù)文件 # 再度調(diào)用，再度調(diào)用，load data sample.raw2photo sample.out# 貯存每一步操作及其運行結(jié)果貯存每一步操作及其運行結(jié)果3sequence 1 2 3 4 5 6 7 8 9 10 11 12# 指定待分析的標記指定待分析的標記4group# 按按LOD3.0, rsequence 1 2 3 5 7# 未知序列未知序列ncompare# 比較比較log-likelihood值的大小，確定最佳排序值的大小，確定最佳排序1: 1 3 2 5 7 like: 0.002: 3 1 2 5 7

7、like: -6.00 20:2 5 3 1 7 like: -52.287sequence 1 3 2 5 78map# 連鎖作圖連鎖作圖 Marker Distance 1 T175 4.2cM 3 C35 15.0cM 2 T93 11.9cM 5 C66 12.2cM 7 T506 43.2 cM 5 Markers log-likelihood=-424.94 9sequence 4 6 8 9 10 11 1210list loci11lod table12sequence 8 9 10 11 1213compare# 得到最佳排列順序得到最佳排列順序 order1: 11 8 1

8、2 9 10# 列出位點列出位點# 顯示表格，劃分亞組顯示表格，劃分亞組# 等同于命令等同于命令suggest subset14sequence order115try 4 6# 試標記試標記4 6的最適位置的最適位置 4 6 0.0 -42.68 11 -35.57 -118.60 8 -19.65 -70.19 12 -46.80 -28.09 9 -51.35 0.00 10 -43.40 -21.09# 最佳順序最佳順序 4 11 8 12 9 6 1016sequence 4 11 8 12 9 6 1017map1.3.2 較復(fù)雜圖譜的制作較復(fù)雜圖譜的制作1prepare data

9、 mouse.raw# 執(zhí)行初始化文件執(zhí)行初始化文件mouse.pre2sequence all3assign# 調(diào)用數(shù)據(jù)文件調(diào)用數(shù)據(jù)文件(含有含有46個個體，個個體，308個標記個標記)# 指定染色體，初始化文件中已錙定了一些標記指定染色體，初始化文件中已錙定了一些標記繼之可決定連鎖標記繼之可決定連鎖標記L016 -anchor locus on chrom12cannot re-assign L036 -assigned to chrom17 at LOD 10.4 A066 -unassigned5sequence unassigned6list status# 顯示未連鎖的標記狀態(tài)顯示

10、未連鎖的標記狀態(tài)Num Name Assignment Chrom LOD181 M228 conflict - -196 M251 unlinked - - 274 A066 unlinked - -4list chromosomesChromosome #Anchors #Total Chrom1 2 18 Chrom2 2 30 Chrom1 2 5 Total: 38 3057linksMarker1 Marker2 Theta LOD cM M228 L038 0.18 3.58 23.00 (chrom3) M228 T010 0.16 5.55 19.13 (chrom14) M

11、228 M032 0.05 11.75 5.28 (chrom14) M251 no linked markers A066 no linked markers8sequence chrom109three pointcont markers log-likelihood difference a-b-c b-a-c a-c-b1: L062 D030 M067 0.00 -8.93 -0.582: L062 D030 M003 -8.63 0.00 -0.74 10order11sequence order112map13sequence chrom10:order114framework

12、chrom1015sequence assigned16place17draw chromosome18quit# 畫出染色體圖譜畫出染色體圖譜# 列出染色體列出染色體10的框架的框架# 安置安置2. MAPMAKER/QTL 1.12.1 運行運行MAPMAKER/EXP 3.0 1load data sample.raw 2run sample.inp 3quit1load data sample.raw2photo quant.out3trait 14show trait5make trait logwt = log(weight)6list traits7s all2. 2 運行運行M

13、APMAKER/QTL 1.18show linkage maps9trait 210scan11draw scan12show peaks13quit2. 2 運行運行MAPMAKER/QTL 1.1vUsing MAPMAKER/EXP vYou 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 gen

14、 and cd to distribution/mapmaker to get the programs. A file sample.raw comes with Mapmaker/EXP. vEach 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 appr

15、opriate subdirectory and proceed with these commands: vprepare data sample.raw Input the data from the raw file. vphoto sample.tutorial Save what you do in a log file. vsequence 1 2 3 4 5 6 7 8 9 10 11 12 Start with all markers. vgroup Group them into linkage groups vsequence 1 2 3 5 7 Use randomly

16、ordered group 1 makers. vcompare Compare all orders. For each in turn, calculate the Likelihood. vsequence 1 3 2 5 7 Decide that this is the best order and specify it. vmap Print the map to the screen. This attaches distances as well. vsequence 4 6 8 9 10 11 12 Now use the rest of the markers. vlist

17、 loci Summarize the number of informative progeny. vlod table Show pairwise distances and linkage LOD scores. vsequence 8 9 10 11 12 Use a randomly ordered subset of markers from group 2. vcompare Compare all orders. For each in turn, calculate the Likelihood. vsequence order1 Use the best order fro

18、m the compare command. vtry 4 6 Try all possible positions of markers 4 and 6. Also, try unlinked idea. vsequence 4 11 8 12 9 6 10 This is the best sequence. vmake chromosome c1 Create chromosome 1. vsequence 1 3 2 5 7 Specify the sequence of markers on chromosome 1. vattach c1 Attach the sequence to chromosome 1. vframework c1 Create the framework (puts in distances) for chromosome 2. vmake chro