fasta2nexus by R script

Workspace loaded from ~/.RData] > setwd("/home/shenzy/work/beast/51samples") > library(seqinr) > data=read.fasta("51strain_core_gene_alignment.aln") > library(ape)  Attaching package: ‘ape’ The following objects are masked from ‘package:seqinr’: as.alignment, consensus[......]

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change the font size of leaf nodes when generating phylogenetic trees using Bio.Phylo.draw()

axes : matplotlib/pylab axes If a valid matplotlib.axes.Axes instance, the phylogram is plotted in that Axes. By default (None), a new figure is created.

This means that you can load your own axes with your size of choice. For example

import matplotlib import matplotlib.pyplot as plt from Bio im[......]

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y叔的ChIP-seq数据分析大礼包(转贴)

熟悉我们生信技能树团队的应该都知道大名鼎鼎的y叔啦,作为我们论坛的荣誉顾问,y叔一直勤勤恳恳的指出我们的错误,特意在此谢谢y叔!并奉上y叔的ChIP-seq数据分析大礼包,已经征得y叔同意啦! 关注Y叔微信公众账号biobabble

CS0: ChIPseq从入门到放弃

接下来要出一个ChIPseq系列,讲一讲ChIPseq和我的ChIPseeker,从入门到放弃是我自己的个人写照。我做ChIPseq总共也就3个月的时间,做的事情并不多,在一知半解的情况下写下了ChIPseeker包。 正如我在《话题投票》里说的,我当时被要求做ChIPseq分析是为他人做嫁衣,而且是[……]

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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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Chip-seq流程报告(转贴)

一、摘要 实验旨在了解Chip-seq的基本原理。通过模仿文献《Targeting super enhancer associated oncogenes in oesophageal squamous cell carcinoma》的流程,学会利用NCBI和EBI数据库下载数据,熟悉Linux下的基本操作,并使用R语言画图,用Python或者shell写脚本进行基本的数据处理,通过FastQC、Bowtie、Macs、samtools、ROSE等软件进行数据处理,并对预测结果进行分析讨论。 二、材料

1、硬件平台

处理器:Intel(R) Core(TM)i7-4710MQ[……]

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Dating a node with BEAST2.0

For details, read http://beast2.cs.auckland.ac.nz/index.php/Main_Page and http://beast2.cs.auckland.ac.nz/index.php/FAQ . For any problem, do not hesitate to browse through the list of questions on the BEAST forum https://groups.google.com/forum/#!forum/beast-users .

Exercise description

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Chip seq

何謂ChIP-Seq? ChIP–seq ( Chromatin immunoprecipitation sequencing )是指染色質免疫沉澱後,所獲得的DNA片段進行高通量定序,並將此片段利用生物資訊的軟體對回至基因體,可以瞭解DNA-binding proteinshistone modifications的狀況,進而得知染色结合的調控因子的相互作用關係。 ChIP-chipChIP-Seq差異? 次世代定序較ChIP-chip提供更高的解析度,較少的雜訊,較少的ChIP-DNA的量,及可偵測的動態範圍及基因體範圍較廣,因此可呈現較真實的基因調控及表觀[……]

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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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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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