Processing a Neuroblastoma cell line data set

In this section, we’ll be working with RNA-seq data from neuroblastoma (NB) cell lines from Harenza, et al. (2017)

The course directors have already processed the raw data using salmon quant and the quant.sf files for each sample can be found in data/NB-cell/salmon_quant/<SAMPLE>.

In the gastric cancer example, we imported Salmon-processed data with tximeta to then use with DESeq2. We will also use DESeq2 for these analyses, specifically for differential expression analysis.

In order to prepare the NB cell line data for differential expression analysis, we will modify the gastric cancer tximeta notebook (02-gastric_cancer_tximeta-live.Rmd) and save this new notebook as nb_cell_tximeta.Rmd:

• To create a new notebook, select File > New File > R Notebook. The new notebook should appear in your Source Pane in RStudio. Save the new notebook, using Ctrl+S (Cmd+S on Mac) or File > Save, in the training-modules/RNA-seq directory with the name nb_cell_line_tximeta.Rmd. You can add a new chunk by clicking the Insert Chunk button on the toolbar or by pressing Cmd+Option+I.

• Alter the code from 02-gastric_cancer_tximeta-live.Rmd to use the NB cell line data. The quant.sf files for each sample can be found in data/NB-cell/salmon_quant/<SAMPLE>.

• Save the tximeta output as data/NB-cell/txi/NB-cell_tximeta.rds. Note that data/NB-cell/txi/ is a new directory.