作图软件的操作

1、第第11讲讲 植物植物QTL作图软件的操作作图软件的操作1. MAPMAKER/EXP 3.01.1 安装和运行安装和运行 复制复制MAPMAKER文件夹到文件夹到C盘盘 解压解压MAPM3PC1.EXE和和MAPM3PC2.EXE压缩包压缩包 双击程序双击程序mapmaker.bat 1.2 数据文件准备数据文件准备源文件（源文件（*.raw）群体：回交群体、群体：回交群体、F2群体、群体、F3群体、群体、RIL群体以及群体以及DH群群体体格式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、体群体类型类型个体数、个体数、标记数和标记数和性状数性状数# 注注释释* 标记标记* 性状性状 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 数据文件准备数据文件准备1. 源文件（源文件（*.raw）*.data，*.map，*.tra*.2pt，*.3pt，*.qtl2. 源文件的中间文件源文件的中间文件1 prep data *.raw*.raw2 load data *.raw1.2 数据文件准备数据文件准备 3. 初始化文件初始化文件1 prep data *.raw*.pre# 定义染色体的数量和名称定义染色体的数量和名称# 锱定标记，指定染色体所属的连锁群锱定标

5、记，指定染色体所属的连锁群# 进行两点测验，为进一步分析提供信息等进行两点测验，为进一步分析提供信息等1.2 数据文件准备数据文件准备 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 简单图谱的制作简单图谱的制作1pr

6、epare data sample.raw# 调用数据文件调用数据文件 # 再度调用，再度调用，load data sample.raw2photo sample.out# 贮存每一步操作及其运行结果贮存每一步操作及其运行结果3sequence 1 2 3 4 5 6 7 8 9 10 11 12# 指定待分析的标记指定待分析的标记4group# 按按LOD3.0, rsequence 1 2 3 5 7# 未知序列未知序列ncompare# 比较比较log-likelihood值的大小，确定最佳排序值的大小，确定最佳排序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# 连锁作图连锁作图 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# 得到最佳排列顺序得到最佳排列顺序 order1: 11 8 1

8、2 9 10# 列出位点列出位点# 显示表格，划分亚组显示表格，划分亚组# 等同于命令等同于命令suggest subset14sequence order115try 4 6# 试标记试标记4 6的最适位置的最适位置 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# 最佳顺序最佳顺序 4 11 8 12 9 6 1016sequence 4 11 8 12 9 6 1017map1.3.2 较复杂图谱的制作较复杂图谱的制作1prepare data

9、 mouse.raw# 执行初始化文件执行初始化文件mouse.pre2sequence all3assign# 调用数据文件调用数据文件(含有含有46个个体，个个体，308个标记个标记)# 指定染色体，初始化文件中已锱定了一些标记指定染色体，初始化文件中已锱定了一些标记继之可决定连锁标记继之可决定连锁标记L016 -anchor locus on chrom12cannot re-assign L036 -assigned to chrom17 at LOD 10.4 A066 -unassigned5sequence unassigned6list status# 显示未连锁的标记状态显示

10、未连锁的标记状态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# 画出染色体图谱画出染色体图谱# 列出染色体列出染色体10的框架的框架# 安置安置2. MAPMAKER/QTL 1.12.1 运行运行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 运行运行M

13、APMAKER/QTL 1.18show linkage maps9trait 210scan11draw scan12show peaks13quit2. 2 运行运行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