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所在平台: Udemy |
课程主页: https://www.udemy.com/course/unix-essentials-for-ngs-bioinformatics/
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**Coursera 课程总结：面向 NGS 生物信息学的 Unix 基础** 本课程旨在向生物科学（尤其是在高通量测序，NGS 数据分析）领域的用户介绍 Unix 作为处理大数据的便捷工具。NGS 技术产生了海量数据，传统的图形用户界面（GUI）工具难以应对，甚至无法打开原始文件。因此，测序数据通常以文本格式生成和存储，以便于处理。 Unix 技能是生物信息学的宝贵财富，它易于使用、效率高且节省大量时间。虽然许多生物信息学专家擅长使用 PERL/PYTHON 等编程语言进行数据分析，但并非所有人都认识到，并非所有任务都需要编写程序。通过 Unix 工具，无需借助高级编程技能和专用软件，即可进行数据处理、为软件准备输入格式，以及便捷地处理和理解分析结果。当然，高级生物信息学分析仍然需要软件和编程技能。 本课程是生物科学研究人员、科学家和 NGS 初学者的绝佳选择。Unix 技能有助于构建数据处理流程（pipelines），将不同的软件组合起来解决特定问题，例如： * 计算和格式化 FASTA 和 FASTQ 序列 * 将多行 FASTA 序列转换为单行 * 从整个数据集中提取所需的 FASTA 和 FASTQ 序列 * 分割和子集化大型序列文件 * 格式化 BLAST、Pfam 和 Interpro 的输出以供分析 * 从基因组文件中提取子序列 * 清理序列文件：修剪和过滤序列 * 生成随机数据集 * 批量处理常用任务 本课程特别关注 Unix 在 NGS 数据处理和项目管理中的特定应用。课程共分四个模块，从基础命令到脚本编写。您将获得大量的实践机会。在四天内，通过教程、视频讲座和练习，您将全面掌握相关技能。讲师采用了最简单易懂的方法，侧重于培养数据处理的思维方式，而非命令的复杂用法。在练习指南中，针对同一任务提供了多种方法，让您有机会体验紧凑和高级的命令选项。 **课程大纲：** * **第一天：NGS 和 Unix 简介** * 课程介绍 * NGS 和 Unix 基础（视频） * Unix：入门、基本命令（目录与文件：创建、删除、导航、列出、读写/检索、解压 NGS 数据文件） * 系统信息相关命令及其用法 * 快速复习 * 练习作业 * 今日挑战 * **第二天：NGS 生物信息学数据探索** * NGS：数据来源、文件和文件格式 * 用于探索的 Unix 命令 * 解决复杂问题的智能技巧 * 快速复习 * 练习作业（与常用 NGS 数据处理任务相关） * 今日挑战 * **第三天：命令的应用** * 文件流和重定向、流编辑器、管道、过滤器 * 权限、符号链接、在终端构建数据处理流程（pipelines） * 练习作业（与常用 NGS 数据处理任务相关） * 今日挑战 * **第四天：批量数据处理** * Shell 脚本简介 * 模式匹配、变量、子 Shell 和循环 * 练习作业（与常用 NGS 数据处理任务相关） * 今日挑战
This course has been designed to introduce Unix to students as most convenient tool for working with big data in biological sciences such as next generation sequencing (NGS) data. NGS technologies are producing massive amount of data in each run which is difficult to handle through GUI based tools, even it is difficult to open raw files. That's why sequencing data are produced and stored in text format for easy handling and processing.Unix skill is an assets for bioinformatics. It is very easy, convenient and save lot of time. Bioinformatics skilled people are knows very well to analyze data with programming language PERL/PYTHON. But all of them not realized that it is not necessary to write program all the time. With the help of unix utilities, data handling and processing, input formatting for software, and easy text processing of results for the understanding can be performed without using high end programming skill and special software's. But you will need software and programming skills for advance bioinformatics analyses. It is great skill for bio-sciences researchers and scientist and NGS beginners. Unix skills will help you in making of pipelines where you can use different software to solve your own objective such asCounting and formatting of fasta and fastq sequencesMultiple line fasta sequences to single line fasta sequencesExtraction of desired fasta and fastq sequences from whole datasetSplitting and subseting of large sequence fileFormatting of blast, pfam, and interpro output for analysisExtraction of sub sequences from genome filesSequence file cleaning: Triming and filtering of sequencesRandom data set generationBulk data processing for common tasks.................and many more common tasksHere, I am intend to cover only specific aspect of unix as required for NGS data processing and project management. Whole course is divided into 4 module from basic command to script. In this course, you will have lot of practice opportunities. In 4 days, you will learn through tutorials, video lectures and assignments for practice. There could be several ways for the teaching and learning, But, i used easiest and simplest approach, and focused to develop thinking for data processing instead of advance and compact use of commands. In guide to practice commands, I have given multiple approach to perform single task. So, you will also have opportunity to use compact and advance options of commands.Day 1 - Introduction to NGS and UNIXCourse introductionBrief description of NGS and UNIX (video).Unix: How to start, basic commands (Directories and files: creation, remove, navigation, listing, writing/retrieval, and unpacking of NGS data files)System information related commands and their usagesQuick revisionPractice assignmentsChallenge of the dayDay 2 - NGS bioinformatics data excursionNGS: data source, files and file formats.Unix command for excursionSmart trick to solve complex problemsQuick revisionPractice assignments (with common NGS data processing related tasks)Challenge of the dayDay 3 - Flying with commandsFile streaming and redirection, stream editor, pipe, filtersPermission, symbolic linking, construction of pipeline on terminal Practice assignments (with common NGS data processing related tasks)Challenge of the dayDay 4 - Bulk data processingBrief introduction of shell scriptingPattern matching, variables, subshells and loopsPractice Assignments (with common NGS data processing related tasks)Challenge of the day
