Skip to content

collection of bioinformatics tools and tips, maybe | 生物信息学软件工具、分析tips集合

License

Notifications You must be signed in to change notification settings

jefferyUstc/WTF-Bioinformatics

Folders and files

NameName
Last commit message
Last commit date

Latest commit

 

History

50 Commits
 
 
 
 
 
 
 
 
 
 

Repository files navigation

目录

Common-Sense

bio-database

  • UCSC
  • ENSEMBL
  • NCBI

sequence-representation

  • Amino-Acid

    A  alanine               P  proline       
    B  aspartate/asparagine  Q  glutamine      
    C  cystine               R  arginine      
    D  aspartate             S  serine      
    E  glutamate             T  threonine      
    F  phenylalanine         U  selenocysteine      
    G  glycine               V  valine        
    H  histidine             W  tryptophan        
    I  isoleucine            Y  tyrosine
    K  lysine                Z  glutamate/glutamine
    L  leucine               X  any
    M  methionine            *  translation stop
    N  asparagine            -  gap of indeterminate length
    

  • Nucleotide

    A  adenosine          C  cytidine             G  guanine
    T  thymidine          N  A/G/C/T (any)        U  uridine 
    K  G/T (keto)         S  G/C (strong)         Y  T/C (pyrimidine) 
    M  A/C (amino)        W  A/T (weak)           R  G/A (purine)        
    B  G/T/C              D  G/A/T                H  A/C/T      
    V  G/C/A              -  gap of indeterminate length
    

suggestion

  1. 建议分析测序数据之前先搞清楚以下两个方面:
    • 原始数据是通过哪种测序平台产生的;它们的错误率分布是怎么样的;是否有一定的偏向性和局限性;是否会显著受GC含量的影响等;
    • 评估它们有可能影响哪些方面的分析;
  2. 从以下方面认识原始测序数据:
    • read各个位置的碱基质量值分布
    • 碱基的总体质量值分布
    • read各个位置上碱基分布比例,目的是为了分析碱基的分离程度
    • GC含量分布
    • read各位置的N含量
    • read是否还包含测序的接头序列
    • read重复率,这个是实验的扩增过程所引入的

About

collection of bioinformatics tools and tips, maybe | 生物信息学软件工具、分析tips集合

Topics

Resources

License

Stars

Watchers

Forks

Releases

No releases published

Packages

No packages published