Install genometools

the ‘new’ error message refers to a nonexistant Cairo library on your system, which is needed for the AnnotationSketch component of GenomeTools. If you do not need this, do a ‘make cleanup’ and recompile with the additional make option ‘cairo=no’, e.g. ‘make errorcheck=no cairo=no’. This will di[……]

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R 列表随意组合 data.frame(x,y)

> protein_data_B30_min<-protein_data[1:2548,10:12] > protein_data_M30_min<-protein_data[1:2548,19:21] > protein_data_30_min<-data.frame(protein_data_B30_min,protein_data_M30_min) > protein_data_30_min[1:2,] B30 B30.1 B30.2 Mgo30 Mgo30.1 Mgo30.2 1 870.5042 867.0873 0 1086.82[......]

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DSK: k-mer counting with very low memory usage

Summary: Counting all the k-mers (substrings of length k) in DNA/RNA sequencing reads is the preliminary step of many bioinformatics applications. However, state of the art k-mer counting methods require that a large data structure resides in memory. Such structure typically grows with the number of[……]

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Free VPN

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Circos for comparative genomes

Circos: nucmer –prefix=refBAV1_qryVScds Dehalococcoides_BAV1.fasta Dehalococcoides_VS.cds.fasta show-tiling -i 80 -c refBAV1_qryVScds.delta > refBAV1_qryVScds.tiling awk -F ” ” ‘{print “chr1″ “\t” $1 “\t” $2}’ refBAV1_qryVScds.tiling > Dehalococcoidessp.VScds.gene_tableBAV1.txt shenzy@s[……]

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How to measure codon usage bias

Codon adaptation index (CAI) is one of them. To examine the CAI value of a gene, a reference table of RSCU (relative synonymous codon usage) values for highly expressed genes is compiled. A software call CodonW, you can download it from: http://codonw.sourceforge.net/. There is also a PhD thesis[……]

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利用tophat和Cufflinks做转录组差异表达分析的步骤详解

今天一个同学给我推荐一篇Nature Protocol 上文章,关于转录组差异表达分析。尚在正式通读之前习惯性浏览一遍图表,说实在这篇文章着实让我觉得有点“另类”。这是一篇活生生的利用Bowtie、tophatCufflinks转录组差异表达分析的protocol。里面详细讲解每一步需要分析什么,用哪些些软件,已经相关命令和参数。 根据文章介绍的workflow,做转录组分析,无论是链特异性转录组数据(Strand-specific RNA-seq)还是非特异性数据,主要内容包括下面几个部分: 1)reads mapping,这里面推荐两款软件一个是Bowtie,另一个是top[……]

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Solexa与Hiseq测序技术中常见术语名词解释

Hiseq测序技术名词解释 第二代测序技术中Solexa以及它的升级版Hiseq,目前使用最多。为了帮助PLoB网友进一步了解Solexa相关的概念。与大家分享一篇网上看到的文章《Solexa测序技术中常见术语解释》,文章后面有参考来源链接。更多相关信息欢迎加入PLoB 2000人的生物信息QQ群(群号:235461986)来讨论,有相关测序以及生物信息学问题需要解答欢迎前来。下面直接附上相关的解释。大家同时可以结合上面的示意图,了解SolexaHiseq的基本结构。 SBS:边合成边测序反应,每次SBS会延伸一个碱基,大约耗时70分钟。 Run:单次上机测序反应,可以产生4G-75G测序通量不等。[……]

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R画 维恩图

 

> install.packages('plotrix') Installing package(s) into ‘/home/shenzy/R/x86_64-pc-linux-gnu-library/2.15’ (as ‘lib’ is unspecified) 试开URL’http://cran.csiro.au/src/contrib/plotrix_3.4-5.tar.gz' Content type 'application/x-gzip' length 211113 bytes (206 Kb) 打开了URL ==================[......]

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hong kong’s meetup

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