作图软件的操作讲解.ppt

第11讲 植物QTL作图软件的操作 1. MAPMAKER/EXP 3.0 1.1 安装和运行 复制MAPMAKER文件夹到C盘 解压MAPM3PC1.EXE和MAPM3PC2.EXE压缩包 双击程序mapmaker.bat 1.2 数据文件准备 源文件（*.raw） 群体：回交群体、F2群体、F3群体、RIL群体以及DH群体 格式data type f2 intercross 20 5 2 #Joe’s tiny data set,10/21 version. *locus1 BBBHH-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 群体 类型 个体数、 标记数和 性状数 # 注 释 * 标记 * 性状 data type f2 intercross 20 5 2 symbols 1=A 3=B 2=H 0=- #Joe’s 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 *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 1.2 数据文件准备 1. 源文件（*.raw） *.data，*.map，*.tra*.2pt，*.3pt，*.qtl 2. 源文件的中间文件 1> prep data *.raw *.raw 2> load data *.raw 1.2 数据文件准备 3. 初始化文件 1> prep data *.raw *.pre # 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 # 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 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 file 1.3 mapmaker/exe 3.0操作流程 1.3.1 简单图谱的制作 1>prepare data sample.raw # 调用数据文件 # 再度调用，>load data sample.raw 2>photo sample.out# 贮存每一步操作及其运行结果 3>sequence 1 2 3 4 5 6 7 8 9 10 11 12# 指定待分析的标记 4>group# 按LOD>3.0, rsequence {1 2 3 5 7} # ｛未知序列｝ncompare # 比较log-likelihood值的大小，确定最佳排序 1: 1 3 2 5 7 like: 0.00 2: 3 1 2 5 7 like: -6.00 … … … … 20:2 5 3 1 7 like: -52.28 7>sequence 1 3 2 5 7 8>map # 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 9>sequence 4 6 8 9 10 11 12 10>list loci 11>lod table 12>sequence {8 9 10 11 12} 13>compare # 得到最佳排列顺序 order1: 11 8 12 9 10 # 列出位点 # 显示表格，划分亚组 # 等同于命令>suggest subset 14>sequence order1 15>try 4 6 # 试标记4 6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 4 11 8 12 9 6 10 16>sequence 4 11 8 12 9 6 10 17>map 1.3.2 较复杂图谱的制作 1>prepare data mouse.raw # 执行初始化文件mouse.pre 2>sequence all 3>assign # 调用数据文件(含有46个个体，308个标记) # 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 L016 -anchor locus on chrom12……cannot re-assign …… …… L036 -assigned to chrom17 at LOD 10.4 …… …… A066 -unassigned 5>sequence unassigned 6>list status # 显示未连锁的标记状态 Num Name Assignment Chrom LOD 181 M228 conflict - - 196 M251 unlinked - - 274 A066 unlinked - - 4>list chromosomes Chromosome #Anchors #Total Chrom1 2 18 Chrom2 2 30 …… …… Chrom1 2 5 Total: 38 305 7>links Marker1 Marker2 Theta LOD cM M228 L038 0.18 3.58 23.00 (chrom3) M228 T010 0.16 5.55 19.13 (chrom14) M228 M032 0.05 11.75 5.28 (chrom14) …… …… M251 no linked markers A066 no linked markers 8>sequence chrom10 9>three point cont markers log-likelihood difference a-b-c b-a-c a-c-b 1: L062 D030 M067 0.00 -8.93 -0.58 2: L062 D030 M003 -8.63 0.00 -0.74 …… …… 10>order 11>sequence order1 12>map 13>sequence chrom10:order1 14>framework chrom10 15>sequence assigned 16>place 17>draw chromosome 18>quit # 画出染色体图谱 # 列出染色体10的框架 # 安置 2. MAPMAKER/QTL 1.1 2.1 运行MAPMAKER/EXP 3.0 1>load data sample.raw 2>run sample.inp 3>quit 1>load data sample.raw 2>photo quant.out 3>trait 1 4>show trait 5>make trait logwt = log(weight) 6>list traits 7>s [all] 2. 2 运行MAPMAKER/QTL 1.1 8>show linkage maps 9>trait 2 10>scan 11>draw scan 12>show peaks 13>quit 2. 2 运行MAPMAKER/QTL 1.1 vUsing 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 genome.wi.mit.edu 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 appropriate 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 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 sp。