Now that you have a brief overview of RNA-seq analysis and one of the most popular bioinformatic softwares available, DESeq2, you will conduct your own demo analysis in order to get a sense of the entire process.
Use the DESeq2 tutorial to recreate the analysis with one of the following data sets:
upload a DESeq2 results table in “.csv” format, with entries sorted by descending Log2FoldChange values and entries with adjusted p-value (padj) <0.075 removed. Please make make sure to annotate your “.rmd” document with what each function/tidbit of code is doing; you will be uploading this R markdown document as part of your notebook check 3.
I will send you the data set.
this is the tutorial for this project
Once you have R Studio installed on your machine, start a new “R Markdown” document:
When you document is loaded, make sure to save it and remember where it is saved – it will have the “.rmd” extension (hint: for the tutorial, one possible option is to create a new folder on your desktop and save the .rmd file in that folder).
Next, download the following RNA-seq data set and make sure to save it in the same location as the “.rmd” file:
Finally, follow along with the tutorial above and make sure to take notes in “markdown” format (see example).
Try to keep the code of each section uniform; to start a new code-chunk, type the following in any blank space of the .rmd document within RStudio:
“`{r}
INSERT CODE FROM TUTORIAL HERE
“`
Once the code has been replicated for each section of the tutorial, the code-chunk can be executed by “running” the chunk with the green arrow located at the top right corner of each code chunk:
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