update to clean up section

Author: aabarug

02-01-ExperimentalPlanning.Rmd

@@ -3,7 +3,9 @@
 
 ## What Is RNAseq
 
-RNAseq is a next generation sequencing technique for profiling all or selected target RNA molecules in a tissue from an organism. It typically involves isolating RNA, converting to cDNA, ligating adapter sequences to the cDNA then amplifying by PCR to construct a library that can be used for sequencing. The reads generated by sequencing are typically aligned to a reference genome.
+RNAseq is a next generation sequencing technique for profiling all or selected RNA molecules in a tissue from an organism. It typically involves isolating RNA, converting to cDNA, ligating adapter sequences to the cDNA then amplifying by PCR to construct a library that can be used for sequencing. The reads generated by a sequencing machine are then aligned to a reference genome and can then be used for analysis. 
+
+A diverse ecosystem of protocols and technology exist that can be used to generate RNAseq data, which can be used in a wide variety of applications. 
 
 (ref:foo1) Overview of the steps in an RNAseq experiment. At each of these steps, there are choices that are made that can influence the final output of the experiment. Image source: [RNA Sequencing Data: Hitchhiker's Guide to Expression Analysis, 2019](https://www.annualreviews.org/content/journals/10.1146/annurev-biodatasci-072018-021255)
 
@@ -13,18 +15,16 @@ knitr::include_graphics("images/experimental_design/overview_rnaseq.png")
 
 ### What is a sequencing machine doing? {- .rationale}
 
-A sequencing machine generates a readout of the nucleotides that make up the original RNA molecule, typically by using uniquely labelled flourescent nucleotides. Every time one of these nucleotides are added to a strand of DNA, the fluorescence emitted is detected by the sequencing machine.
-
+A sequencing machine generates a readout of the nucleotides that make up a DNA fragement. The most common type of sequencing is Sequencing by Synthesis which involves the use of unique fluorescently labelled nucleotides. These nucleotides are added one at a time and every time one of these nucleotides are added to a strand of DNA, the fluorescence emitted is detected by the sequencing machine.
 
 (ref:foo2) Illumina Sequencing by Synthesis. Image source: [Microbenotes: Illumina Sequencing](https://microbenotes.com/illumina-sequencing/)
 
 ```{r, echo=FALSE, out.width="90%", fig.cap="(ref:foo2)"}
 knitr::include_graphics("images/experimental_design/fig_illumina_sequencing.png")
 ```
 
-##
 
-A diverse ecosystem of protocols and technology exist that can be used to generate RNAseq data, which can be used in a wide variety of applications. 
+
 
 
 ## Planning an RNAseq Experiment