如何读懂和利用你的微生物多样性测序结果?

16s分析结果详解 很多小伙伴有过这样的经历,在拿到公司出具的报告之后,仍然一头雾水,几十页的报告内容看着丰富却不知该怎么运用。我们一起来理一下关键图表的含义OTU是我们要搞清的一个重要概念,可以说是后续分析的基石。 OTU(operational taxonomic units) 是在系统发生学研究或群体遗传学研究中,为了便于进行分析,人为给某一个分类单元(品系,种,属,分组等)设置的同一标志。通常按照 97% 的相似性阈值将序列划分为不同的 OTU,每一个 OTU 通常被视为一个微生物物种。相似性小于97%就可以认为属于不同的种,相似性小于93%-95%,可以认为属于[……]

Read more

[…]

Cytoscape基础教程笔记

昨天开始学用Cytoscape,其tutorial分为两个部分,基础的和高级的。基础教程又分成了四课:Getting Started、Filters & Editor、Fetching External Data和Expression Analysis。为防忘记,做个摘记。

第一课 新手上路,地址见http://goo.gl/FJLxp。 Cytoscape可以本地安装,也可以web start。软件得用java,所以要装JRE。我在Ubuntu下装了OpenJDK,可以运行。因为以前一直没把jnlp文件和java关联起来,所以从没成功web start过,试了一下“课文”[……]

Read more

[…]

Reading the NCBI’s GEO microarray SOFT files in R/BioConductor

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/geo/ This page discusses how to load GEO SOFT format microarray data from the Gene Expression Omnibus database (GEO) (hosted by the NCBI) into R/BioConductor. SOFT stands for Simple Omnibus Format in Text. There are actually four[……]

Read more

[…]

RSeQC: quality control of RNA-seq experiments

Abstract

Motivation: RNA-seq has been extensively used for transcriptome study. Quality control (QC) is critical to ensure that RNA-seq data are of high quality and suitable for subsequent analyses. However, QC is a time-consuming and complex task, due to the massive size and versatile nature of RN[……]

Read more

[…]