https://github.com/jefferyustc/wtf-bioinformatics

collection of bioinformatics tools and tips, maybe | 生物信息学软件工具、分析tips集合
https://github.com/jefferyustc/wtf-bioinformatics

bioinformatics bioinformatics-analysis

Last synced: about 2 months ago
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collection of bioinformatics tools and tips, maybe | 生物信息学软件工具、分析tips集合

• Host: GitHub
• URL: https://github.com/jefferyustc/wtf-bioinformatics
• Owner: jefferyUstc
• License: gpl-3.0
• Created: 2018-12-09T14:25:52.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2021-03-26T02:41:08.000Z (almost 4 years ago)
• Last Synced: 2023-10-20T05:40:44.802Z (about 1 year ago)
• Topics: bioinformatics, bioinformatics-analysis
• Homepage:
• Size: 19.5 MB
• Stars: 10
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
## 目录

- [Tools](docs/Tools.md)

- [How_To_Read_Paper](docs/ReadPaper.md)

- [File_Format](docs/FileFormat.md)

- [Common-Sense](#Common-Sense)

  * [bio-database](#bio-database)

  * [sequence-representation](#sequence-representation)

  * [suggestion](#suggestion)

# Common-Sense

### bio-database

- UCSC

- ENSEMBL

- NCBI

### sequence-representation

- Amino-Acid

  > ```text

  > 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

  > ```text

  > 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