bioinformatics
weixin_42953727
Where there is a will, there is a way
展开
-
生信学习网站推荐
I’m back!好久不更新博客了,不过学习依旧持续着B站上有好多免费的生信课程,最近在学习“生信技能树”出品的生信教程,很干货,收获很多,推荐给初学的小伙伴们。生命不息,学习不止,想学好生信在于多听多看和多多练习,同时不断思考,保持兴趣。这一阶段的目标是复现文章数据分析,加油!...原创 2020-10-15 22:40:57 · 760 阅读 · 3 评论 -
Lecture 5——DNA-seq-2_Bioinformatics and Statistical Topics
本文图片来自于学习视频——新一代测序技术数据分析第五讲 DNA-seq2_Bioinformatics and Statistical TopicsSequence mappabilityHuman genomeThe minimum length (number of nucleotides) can be uniquely mapped back to human genome?In...原创 2019-10-15 09:29:46 · 958 阅读 · 0 评论 -
Lecture 3——DNA-seq-1
本文图片来自于学习视频——新一代测序技术数据分析第三讲 DNA-seqReviewAlignment srategiesSmith-Waterman(speed too slow to use)Fast alignmentHash tableSeed and extensionMask(for mismatches)Suffix tree/prefix treeSuffix ar...原创 2019-10-14 08:44:12 · 808 阅读 · 0 评论 -
Lecture 2——Basics of data processing
本文图片来自于学习视频——新一代测序技术数据分析第二讲Lecture 2——Basics of data processingReview Lecutre 1OutlineDate analysis workflowSequence qualify evaluationPhred scoresNGS error ratesAlignmentSmith-Waterman algo...原创 2019-10-11 20:36:07 · 413 阅读 · 0 评论 -
Bioinformatics with Python Cookbook.1
Chapter 1 Python and the Surrounding Software Ecology本章主要介绍linux上Python及周边软件的安装,为此,应先了解linux系统版本信息以及已经安装了哪些软件,若已经安装了Python,但仍想通过Anaconda安装Python,最好unset PYTHONPATH,或者卸载已安装的Python和libraries。查看Linux版...原创 2019-09-25 19:11:39 · 359 阅读 · 0 评论 -
next-generation sequencing analysis method——paper1
半路出家会有很多困惑,我想若要踏实基础,一步步了解二代测序所有过程,读paper应该是正统。因此今天在Web of Science中检索"next-generation sequencing analysis method",找到多篇关于二代测序的发展历史,分析方法及应用等方面的文章,并在读后记录下来心得,应该会有所提高。第一篇:来自于:Omics Technologies and Bio-...原创 2019-09-26 21:47:45 · 590 阅读 · 0 评论 -
next-generation sequencing analysis method——paper2
Here, we outline some of the tools and databases commonly used for the analysis of next-generation sequence data with comment on their utility.GENOME ASSEMBLYALGORITHMS(1)SSAKE: one of the first sh...原创 2019-09-28 19:15:12 · 295 阅读 · 0 评论 -
next-generation sequencing analysis method——paper3
Abstract: available software to align reads to a reference; use resulting alignments to call, annotate, view, and filter small sequence variants; variant calling includes read alignment with novoalig...原创 2019-10-02 14:14:16 · 598 阅读 · 0 评论 -
山大公开课笔记2
第五节 蛋白质数据库一、一级蛋白质数据库一级蛋白质序列数据库swissprot、TrEMBL、PIR 三者共同构成UNIPROT(1)swissprot: 一个人工注释的蛋白质序列数据库,拥有注释可信度高、冗余度小的优点。由欧洲生物信息学研究生EMBL-EBI与瑞士生物信息学研究生SIB共同管理。(2)TrEMBL(translation from EMBL): 一个计算机注释的蛋白质...原创 2019-10-08 20:10:03 · 773 阅读 · 0 评论 -
山大公开课学习笔记3
软件预测蛋白质二级结构通过氨基酸序列,预测蛋白质二级结构常用软件:PSIPRED、Jpred3、PREDICTPROTEIN、SSpro、PSSpred、PREDATOR、GOR V蛋白质的三级结构测定主要方法:X射线衍射法、核磁共振法(分子量小的蛋白质)等PDB检索,或Advanced search蛋白质三级结构可视化软件Pymol、VMD(免费)、Maestro、CanvasM...原创 2019-10-09 10:52:47 · 588 阅读 · 0 评论 -
山大公开课——高通量测序1
Sequencing bias/errors1. 产生原因454:识别不同荧光信号,不易区分homopolymerIllumina:当分子簇形成数量较少时,不能灵敏地捕获荧光信号;及信号冲突,对于High GC区域的覆盖度比较低。2. 解决方法(Correcting errors in short reads by multiple alignments/ Quake: quality-a...原创 2019-10-09 14:59:08 · 429 阅读 · 0 评论 -
山大公开课笔记——数据挖掘
数据挖掘一、三要素:1. 统计2. 数据库系统3. 机器学习数据库系统 DBS(Database System)数据库管理系统 DBMS(Database Management System)+ 数据库 DB(Database)= DBSsoftware for management data storage二、常用的数据库系统:1. 关系型数据库系统:e.g. ...原创 2019-10-09 20:00:38 · 343 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-12
Chapter12 Bioinformatics Shell Scripting, Writing Pipelines, and Parallelizing TasksWe’ll see how to write rerunnable Bash shell scripts, automate fileprocessing tasks with find and xargs, run pipeli...原创 2019-09-13 14:47:42 · 364 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-11-2
接上一篇Chapter 11Visualizing Alignments with samtools tview and the Integrated Genomics ViewerSamtools tview requires position-sorted and indexed BAM files as input.原创 2019-09-09 21:59:49 · 681 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-3
Chapter 3 Remedial Unix Shell== In this chapter, we’ll cover remedial concepts that deeply underly how we use the shell in bioinformatics: streams, redirection, pipes, working with running programs,...原创 2019-08-24 21:06:00 · 351 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-4、5
Chapter4 Working with Remote MachinesMaintaining Long-Running Jobs with nohup and tmux1. nohupBecause the nohup command is catching and ignoring these hangup signals, the program you’re running won...原创 2019-08-25 14:37:12 · 199 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-6
Chapter6 Bioinformatics DataRetrieving Bioinformatics DataDownloading Data with wget and curlTwo common command-line programs for downloading data from the Web are wget and curl. Depending on your ...原创 2019-08-25 17:28:30 · 482 阅读 · 1 评论 -
Bioinformatics Data Skills by Oreilly——学习生信的入门好书
翻阅《生信宝典》公众号,偶然看到推荐的两本生信入门好书,分享给大家:《Bioinformatics Data Skills - - Reproducible.and.Robust.Research.with.Open.Source.Tools》链接:》链接: 接: https://pan.baidu.com/s/1c2g0MPU 密码: 密码: v2c9《Bioinformatics wi...原创 2019-08-21 22:17:10 · 3121 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-1
Chapter1. How to learn bioinformatics看起来是琐碎的小技巧,甚至是关于信仰的东西,可能要真正投入进去,才能慢慢体会,看得不太认真,许多略过的东西,以后可以再回头看。Test Code, or Better Yet, Let Code Test Code学到了用Code test code:...原创 2019-08-22 20:20:12 · 499 阅读 · 2 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-7-1
PART III Practice: Bioinformatics Data SkillsChapter7 Unix Data ToolsInspecting and Manipulating Text Data with Unix ToolsIn this chapter, we’ll work with very simple genomic feature formats: BED (...原创 2019-08-26 21:31:24 · 359 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-7-2
接上一篇Chapter 7The All-Powerful Grepgrep “pattern” files–color=autogrep 是贪婪匹配,用**-w**进行准确匹配(constraining our matches to be words),默认输出行。$ cat example.txtbiobioinfobioinformaticscomputational ...原创 2019-08-29 21:37:04 · 364 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-7-3
接上一篇Chapter7Text Processing with AwkTwo basic concepts——records and fields, and pattern-action pairsAssigns the entire record to the variable $0, and field one’s value is assigned to $1, field two’...原创 2019-08-31 21:46:59 · 256 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-7-4
接上一篇Chapter7Advanced Shell TricksSubshells$ echo "this command"; echo "that command" | sed 's/command/step/'this commandthat step$ (echo "this command"; echo "that command") | sed 's/command/ste...原创 2019-08-31 22:10:02 · 181 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-9
Chapter9 Working with Range DataA Crash Course in Genomic Ranges and Coordinate SystemsCrossMap is a command-line tool that converts many data formats (BED, GFF/ GTF, SAM/BAM, Wiggle, VCF) between c...原创 2019-09-01 17:07:11 · 202 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-10
Chapter 10 Working with Sequence DataNucleotide (and protein) sequences are stored in two plain-text formats widespread in bioinformatics: FASTA and FASTQ—pronounced fast-ah (or fast-A) and fast-Q, r...原创 2019-09-03 21:03:21 · 590 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-11-1
Chapter 11 Working with Alignment Data突然觉得这是一本比较基础的且要有耐心才能看下去的书,但作者介绍的比较繁琐,没有直入主题,基本的分析流程和背景并不太成体系。有基础的人甚至可以直接跳到11章,想快点看完进入下一本了。The Sequence Alignment/ Mapping (SAM) format for mapping data (and its...原创 2019-09-08 17:09:55 · 741 阅读 · 0 评论 -
Bioinformatics Data Skills by Oreilly学习笔记-2
Chapter2 Setting Up and Managing a Bioinformatics ProjectOrganizing Data to Automate File Processing TasksShell Expansion Tips$ echo dog-{gone,bowl,bark}dog-gone dog-bowl dog-bark$ mkdir -p zm...原创 2019-08-23 20:09:13 · 255 阅读 · 0 评论