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18. Schatzlab CSH Genomes

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发表于 2016-9-2 15:12:15 | 显示全部楼层 |阅读模式
本帖最后由 happylittlepig 于 2016-9-2 21:11 编辑

基因组拼接、测序技术原理等
推荐指数3
Teaching

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·  2013
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·  Special Topics



About Schatzlab
MichaelSchatz创办。Michael Schatz个人是彭博社计算科学和生物学杰出副教授,他本人也有在约翰霍普金斯大学和冷泉港实验室任职。




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 楼主| 发表于 2016-9-2 15:12:42 | 显示全部楼层

Exercises

Beyond the Genome Challenges
Identify the virus in a cancer exome sequencing project
Identify the secret message inserted into a microbial genome
Identify the secret message encoded as variants within a metagenomics sample
Genomics
Read mapping, identifying variants, running BWA/SAMTools
Read mapping, computing expression, running Bowtie/Tophat/Cufflinks
De novo assembly and error correction, whole genome alignment
Coverage analysis using plane-sweep algorithms
Probability and Statistics
Uniform Random Probability
Binimal and Normal Distributions
Poisson Distribution
Exponential Distribution
Computing
Introduction to python, variables, lists, conditions, loops
Brute force search, dictionaries, motif finding
Getting started with Hadoop, kmer counting and word analysis





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 楼主| 发表于 2016-9-2 15:13:09 | 显示全部楼层
Essential Resoures

Online Resources
PubMed, Genomes, Genbank, SRA
Interactive genome plots, coverage, annotations
Interactive genome analysis (CSHL version)
Forums and tutorials for genomics analysis
Videos and Tutorials on many science and mathematics related topics
Social networking for citations and papers
Programming and Bioinformatics exercises
iPython Notebooks of basic string algorithms
FASTQ trimming and error correction
Filter and trim fastq files
Error Correction of Short Reads


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 楼主| 发表于 2016-9-2 15:13:36 | 显示全部楼层
Aligners and variant callers
Ultra-fast short read mapping with the BWT
Feature rich short read alignment
SAM/BAM alignment filtering and scoring
SAM/BAM alignment filtering
Slice and dice genomics intervals
Variant calling
Structural Variations calling with discordant pair analysis
RNA-seq Analysis
Spliced alignment for RNA-seq
Transcript assembly and quantification
De novo transcript assembly and quantification


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 楼主| 发表于 2016-9-2 15:14:33 | 显示全部楼层
  
Assembly and Whole Genome Alignment
  
      
  
  
Assembly of short reads
  
      
  
  
Assembly of short reads
  
      
  
  
Assembly of long reads
  
      
  
  
Whole Genome Alignment
  
      
  
  
Assembly and assembly related tools
  
  
  
  
Statistics and Visualization
  
      
  
  
Python Integrated Development Environment
  
      
  
  
Visualization in python
  
      
  
  
Statistics and visualization
  
      
  
  
Circular plots of genomes and other data
  
      
  
  
Layout and render graphs
  
      
  
  
Data Mining and classification
  
      
  
  
Interactive Genomics Viewer for short reads
  

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