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