Good software

multiqc   ranger    ployly https://github.com/MultiQC https://github.com/ranger/ranger https://zhuanlan.zhihu.com/p/34369349 […]

Data Binning and Plotting

In statistics, data binning is a way to categorize a number of continuous values into a smaller number of buckets (bins). Each bucket defines an numerical interval. For example, if there is a variable about house-based education levels which are measured by continuous values ranged between 0 and 19,[……]

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ChIPseeker for ChIP peak annotation (转贴)

https://guangchuangyu.github.io/2014/04/chipseeker-for-chip-peak-annotation/ ChIPpeakAnno WAS the only R package for ChIP peak annotation. I used it for annotating peak in my recent study. I found it does not consider the strand information of genes. I reported the bug to the authors, but they[……]

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Mapping reads with bwa and bowtie

In this tutorial, we’re going to take a set of Illumina reads from an inbred Drosophila melanogaster line, and map them back to the reference genome. (After these steps, we could do things like generate a list of SNPs at which this line differs from the reference strain, or generate a genome sequenc[……]

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BACTERIAL GENOMICS TUTORIAL (repost)

[Originally posted by Kat on her BacPathGenomics blog, April 2013] This is a shameless plug for an article and accompanying tutorial I’ve just published together with David Edwards, my excellent MSc Bioinformatics student from the University of Melbourne. It’s currently available as a PDF pre-pub[……]

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POPULATION GENOMICS OF KLEBSIELLA (Repost)

https://holtlab.net/2015/06/23/population-genomics-of-klebsiella/ Well, after almost 6 years, our Klebsiella pneumoniae genomics paper is finally out! It’s a beast of a thing and there are still a million and one questions to address just from this one data set. For those interested in looking[……]

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TOOLS FOR BACTERIAL COMPARATIVE GENOMICS

Yesterday I spoke at a workshop for JAMS TOAST (Sydney’s Joint Academic Microbiology Seminars – bioinformatics workshop)… I was asked to cover tools for comparative genomics, so I put together a list of the tried and tested programs that I find most useful for this kind of analysis. So here is the l[……]

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Bowtie2-manual (转贴)

getting started with Bowtie 2: Lambda phage example-从这里开始使用Bowtie2:λ噬菌体的例子

Bowtie2自带了一些入门级的示例文件,这些示例文件并不具有科学含义,我们用λ噬菌体的参考基因组只是因为它很短,并且例子里面的reads是由一个电脑程序生成的而不是测序的结果。但是,这些文件能让你立即开始运行Bowtie2和下游的程序。 首先按照获取Bowtie2的指导下载它。设置Bowtie2环境变量BT2_HOME,把它指向含有bowtie2, bowtie2-buildbowtie2-inspect二进制文件的新Bowtie2的[……]

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RNA-seq :TopHat2 + Cufflinks分析流程 (转帖)

RNA-seq :TopHat2 + Cufflinks分析流程:    1、测序数据质量控制:fastqc软件       1)使用方法:/life/rjian/software/fastQC/FastQC/fastqc -o /life/rjian/data/liyan/filename_fastqc \filename.fq >>filename.log       2)参数说明:-o:输出文件所在目录,并且是已经存在的目录,如:filename_fastqc                    –noextract:不解压缩输出文件              [……]

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用DESeq进行差异分析的源代码

要保证当前文件夹下面有了742KO1.count等4个文件,就是用htseq对比对的bam文件进行处理后的输出文件 library(DESeq) #加载数据 K1=read.table(“742KO1.count”,row.names=1) K2=read.table(“743KO2.count”,row.names=1) W1=read.table(“740WT1.count”,row.names=1) W2=read.table(“741WT2.count”,row.names=1) #列名 data=cbind(K1,K2,W1,W2) #如果是htseq的结果,则[……]

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