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+#Commands run on wynton in session 1 of the Intro to RNA-seq data analysis workshop
+
+#upload the data to wynton using data transfer (or dt) node
+{local}$ scp -r Downloads/Intro_to_RNA-seq_data_analysis/ alice@dt2.wynton.ucsf.edu:~
+
+#login to the wynton cluster
+{local}$ ssh alice@log2.wynton.ucsf.edu
+#enter your wynton password when prompted and hit enter
+
+#once you are logged in to wynton,
+#list the contents of the home diretory or ~
+#the uploaded folder Intro_to_RNA-seq_data_analysis shoudl appear in the result
+[alice@log2 ~]$ ls
+
+#login to the development node
+[alice@log2 ~]$ ssh dev3 
+
+#list the contents of the Intro_to_RNA-seq_data_analysis folder
+[alice@dev3 ~]$ ls Intro_to_RNA-seq_data_analysis/
+
+#go to the Intro_to_RNA-seq_data_analysis folder
+[alice@dev3 ~]$ cd Intro_to_RNA-seq_data_analysis/
+
+#search for fastqc on wynton
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ module spider fastqc
+
+#check how to load fastqc/0.11.9
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ module spider fastqc/0.11.9
+
+#load the CBI module before loading fastqc
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ module load CBI
+
+#load the fastqc/0.11.9 module
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ module load fastqc/0.11.9
+
+#check if the right version of fastqc is loaded
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ fastqc --version
+
+#check the documentation of fastqc
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ fastqc --help
+
+#run fastqc on the Bacteria_GATTACA_L001_R1_001.fastq file
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ fastqc Bacteria_GATTACA_L001_R1_001.fastq
+
+#once the above command completes running,
+#check the output - there should be 2 output files
+#   1. Bacteria_GATTACA_L001_R1_001_fastqc.html
+#   2. Bacteria_GATTACA_L001_R1_001_fastqc.zip
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ ls
+
+#download the results from wynton to Downloads folder on local computer 
+#open a new terminal (MacOS) or command prompt (Windows) window 
+{local}$ scp aagrawal@dt2.wynton.ucsf.edu:~/Intro_to_RNA-seq_data_analysis/Bacteria_GATTACA_L001_R1_001_fastqc.html Downloads
+
+{local}$ scp aagrawal@dt2.wynton.ucsf.edu:~/Intro_to_RNA-seq_data_analysis/Bacteria_GATTACA_L001_R1_001_fastqc.zip Downloads
+
+#go back to the terminal (MacOS) or command prompt (Windows) window where you are logged in to wynton
+#we will build a singularity container using the docker image from https://hub.docker.com/r/nfcore/rnaseq/
+#this should take a couple of minutes to complete
+# we will look at the output of this command in session 2
+[alice@dev3 Intro_to_RNA-seq_data_analysis]$ singularity build rna_seq_container.sif docker://nfcore/rnaseq 
+
+
+############## END SESSION 1 ##############
+