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wiki:alignment1 [2018/11/15 06:03]
erin
wiki:alignment1 [2018/11/15 09:02] (current)
erin
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   * Quiz   * Quiz
-  * Homework commentary +  * Assignment Commentary 
-  * +  * Sequencing doo dads 
 +  * Assignment Slides
  
-====== Alignment ====== 
  
-Let's take a step back and review our goals and strategy. ​+---- 
 + 
 + 
 +====== Alignment ======
  
 Our goal ... to take sequenced samples from an RNA-seq experiment and process those sequences so we can determine the answers to biological questions. Our goal ... to take sequenced samples from an RNA-seq experiment and process those sequences so we can determine the answers to biological questions.
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 Here is our strategy map... Here is our strategy map...
  
-{{ :wiki:map_big.jpg?​direct&​600 |}}+{{ :wiki:pipeline_for_this_course.jpg?​direct&​600 |}} 
  
 Today, we're going to talk about aligning the reads to a reference genome. For today'​s purposes, we can focus on just one branch of this process here... Today, we're going to talk about aligning the reads to a reference genome. For today'​s purposes, we can focus on just one branch of this process here...
  
-{{ :wiki:map_smaller.jpg?​direct&​500 |}}+{{ :wiki:pipeline_for_this_course_2.jpg?​direct&​400 |}} 
 + 
 +---- 
 + 
 +====== Example Data ====== 
 + 
 +**The dataset we will use is:** 
 + 
 +RNA-seq-based transcriptomic and metabolomic analysis reveal stress responses and programmed cell death induced by acetic acid in Saccharomyces cerevisiae. 
 +Dong Y, Hu J, Fan L, and Chen Q. (2016) Scientific Reports. 7:4. DOI: [[https://​www.ncbi.nlm.nih.gov/​pubmed/​28209995|10.1038/​srep42659]]. 
 + 
 + 
 +{{ :​wiki:​dong_srep42659.pdf |}} 
 + 
 + 
 +Here is the structure of the data: 
 + 
 +{{ :​wiki:​data_structure.jpg?​direct&​500 |}} 
  
-[[|{{:wiki:hisat2build|slide2_arrow.png?​40|}}]] [[wiki:​hisat2build|Building ​hisat2 ​genome indices]]+[[wiki:​hisat2build|{{:​wiki:​slide2_arrow.png?​40|}}]][[wiki:​hisat2build|Building ​HISAT2 ​genome indices]]
  
wiki/alignment1.1542286982.txt.gz · Last modified: 2018/11/15 06:03 by erin