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wiki:alignment1 [2018/11/08 08:42]
erin created
wiki:alignment1 [2018/11/15 09:02] (current)
erin
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-====== Alignment ​======+====== Intro Activities ====== 
 + 
 +  * Quiz 
 +  * Assignment Commentary 
 +  * Sequencing doo dads 
 +  * Assignment Slides 
 + 
 + 
 +---- 
 + 
 + 
 +====== 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 strategy ... to use a series of computational algorithms to align the reads to the genome, tabulate the number of reads associated with each gene, and use statistical methods to determine significantly differentially abundant transcripts. 
 + 
 +Here is our strategy map... 
 + 
 +{{ :​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... 
 + 
 +{{ :​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|{{:​wiki:​slide2_arrow.png?​40|}}]][[wiki:​hisat2build|Building HISAT2 genome indices]] 
wiki/alignment1.1541691772.txt.gz · Last modified: 2018/11/08 08:42 by erin