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Mothur命令中文解释——Mothur中文简易教程 Mothur命令教程 从这个页面http://www.mothur.org/wiki/Category:Commands 上查阅的所有命令，根据个人理解翻译了一下。个人能力有限，会有不当之处。 A-G (查看时请用Ctrl+F快捷键) Align.check 这个命令使你计算16S rRNA基因序列中潜在的错配碱基对数目。如果你对ARB(http://www.arb-home.de/)的编辑窗口熟悉的话，这与计算~，#，-和=这些符号的数目相同。用greengenes的二级结构图谱和esophagus dataset[……] […] trim.seqs(fasta=CN.fa,qfile=CN.quala, maxambig=0, maxhomop=8, flip=T, bdiffs=1, pdiffs=2, qwindowaverage=35, qwindowsize=50, processors=7) system(./grupp_CN.pl CN.trim.fasta > CN.groups) unique.seqs(fasta=CN.trim.fasta) align.seqs(fasta=CN.trim.unique.fasta, reference=gg.ref.fasta, processors=[……] […] Align.check 这个命令使你计算16S rRNA基因序列中潜在的错配碱基对数目。如果你对ARB(http://www.arb-home.de/)的编辑窗口熟悉的话，这与计算~，#，-和=这些符号的数目相同。用greengenes的二级结构图谱和esophagus dataset运行这个命令。要运行这个命令，你必须提供FASTA格式的序列文件。 Align.seqs 这个命令把用户提供的FASTA格式的候选序列文件对齐到用户提供的同样格式的模板序列。通用的方法是： 1.采用kmer searching（http://sourceforge.net/apps/mediawiki/k[……] […] # --Dot/Line graphs-- # We might be interested in plotting the first two dimensions of a PCoA or # NMDS plot. Let's do this with data generated in the Costello stool analysis # tutorial. The necessary file is in your folder. nmds<-read.table(file="stool.final.an.thetayc.0.03.lt.nmds.axes[......] […] Our project TaxCollector has been published in MPDI Diversity. Abstract The high level of conservation of 16S ribosomal RNA gene (16S rRNA) in all Prokaryotes makes this gene an ideal tool for the rapid identification and classification of these microorganisms. Databases such as the Ribosomal Da[……] […] http://www.bioconductor.org/packages/release/bioc/html/mcaGUI.html mcaGUIMicrobial Community Analysis GUIBioconductor version: Release (2.10) Microbial community analysis GUI for R using gWidgets. Author: Wade K. Copeland, Vandhana Krishnan, Daniel Beck, Matt Settles, James Foster, Kyu-Ch[……] […] step1:通过mothur 中的summary.seqs 可以很方便获取长度分布信息 mothur > summary.seqs(fasta=AMIgene_11a.pep) Start End NBases Ambigs Polymer NumSeqs Minimum: 1 20 20 16 4 1 2.5%-tile: 1 55 55 42 8 35 25%-tile: 1 144 144 112 14 350 Median: 1 242 242 189 17 699 75%-tile: 1 380 380 293 21 1048 97.5%-tile: 1[……] […] |
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