From 802ca6682bbadf1262f86f377b654db365a85af1 Mon Sep 17 00:00:00 2001 From: Ayushi Agrawal <88406934+ayushi-agrawal-gladstone@users.noreply.github.com> Date: Wed, 13 Jul 2022 16:07:58 -0700 Subject: [PATCH] Delete steps_on_wynton_session1.txt --- intro-rna-seq/steps_on_wynton_session1.txt | 65 ---------------------- 1 file changed, 65 deletions(-) delete mode 100644 intro-rna-seq/steps_on_wynton_session1.txt diff --git a/intro-rna-seq/steps_on_wynton_session1.txt b/intro-rna-seq/steps_on_wynton_session1.txt deleted file mode 100644 index c9dc206..0000000 --- a/intro-rna-seq/steps_on_wynton_session1.txt +++ /dev/null @@ -1,65 +0,0 @@ -#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 ############## -