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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getfasta (bedtools)

getfasta

../../_images/getfasta-glyph.pngbedtools getfasta extracts sequences from a FASTA file for each of the intervals defined in a BED/GFF/VCF file.

Tip

1. The headers in the input FASTA file must exactly match the chromosome column in the BED file. 2. You can use the UNIX fold command to set the line width of[……]

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Quick guide for parameters in tophat-cufflinks in nematode RNA-seq analysis

The summary of tophat-cufflinks protocol is like that:

step1: generate a tophat_out folder with bam files

tophat -G genes.gtf <index> sample1_1.fq sample1_2.fq tophat -G genes.gtf <index> sample2_1.fq sample2_2.fq 

step2: generate new .gtf files (assemble isoform)

c[......]

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