wiki:alignment1

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 wiki:alignment1 [2018/11/14 09:28]erin wiki:alignment1 [2018/11/15 09:02] (current)erin Both sides previous revision Previous revision 2018/11/15 09:02 erin 2018/11/15 09:01 erin 2018/11/15 08:59 erin 2018/11/15 08:58 erin 2018/11/15 08:57 erin 2018/11/15 08:55 erin 2018/11/15 08:55 erin 2018/11/15 06:47 erin 2018/11/15 06:03 erin 2018/11/15 06:03 erin 2018/11/15 06:02 erin 2018/11/14 09:28 erin 2018/11/08 15:42 erin 2018/11/08 15:42 erin 2018/11/08 15:42 erin 2018/11/08 15:25 erin 2018/11/08 08:42 erin created Next revision Previous revision 2018/11/15 09:02 erin 2018/11/15 09:01 erin 2018/11/15 08:59 erin 2018/11/15 08:58 erin 2018/11/15 08:57 erin 2018/11/15 08:55 erin 2018/11/15 08:55 erin 2018/11/15 06:47 erin 2018/11/15 06:03 erin 2018/11/15 06:03 erin 2018/11/15 06:02 erin 2018/11/14 09:28 erin 2018/11/08 15:42 erin 2018/11/08 15:42 erin 2018/11/08 15:42 erin 2018/11/08 15:25 erin 2018/11/08 08:42 erin created Line 2: Line 2: * 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. Line 15: Line 18: 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|{{:​wiki:​slide2_arrow.png?​40|}}]][[wiki:​hisat2build|Building HISAT2 genome indices]]