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intro-rna-seq/all_steps_docker_desktop.sh

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+#!/bin/bash
+
+# This script should be run on your local laptop or computer
+# Please make sure you have installed Docker Desktop using the instructions at: https://www.docker.com/products/docker-desktop/
+# Before running this script, do the following
+##  1. open the Docker Dekstop and make sure it is running
+##  2. open a new terminal (MacOS) or command prompt (Windows) window 
+
+#check if docker is running
+#the below command will print out the docker version if docker is running
+docker --version
+
+#get the docker image from https://hub.docker.com/r/nfcore/rnaseq/
+#we will be using this image for all the analyses
+docker pull nfcore/rnaseq 
+
+#check if the docker image was downloaded successfully
+docker images
+
+#spin up a docker container
+##for M1 chip mac, use the below command
+docker run --platform linux/amd64 --name rna_bash --rm -it -v ~/Downloads/Intro_to_RNA-seq_data_analysis:/home nfcore/rnaseq bash
+##for all other computers, use the below command
+docker run --name rna_bash --rm -it -v ~/Downloads/Intro_to_RNA-seq_data_analysis:/home nfcore/rnaseq bash
+
+#a new prompt will apear and the conatiner is now active
+#the home directory should have all the contents of ~/Downloads/Intro_to_RNA-seq_data_analysis
+#go to the home directory in the docker container
+cd home
+
+#run fastqc
+fastqc Bacteria_GATTACA_L001_R1_001.fastq
+
+#trim the reads using cutadapt
+cutadapt -a file:Adapter_Sequence.fasta -o trimmed.fastq Bacteria_GATTACA_L001_R1_001.fastq
+
+#run fastqc on the trimmed reads
+fastqc trimmed.fastq
+
+#create a new folder
+mkdir star_index
+
+#create the STAR index
+STAR --runMode genomeGenerate --genomeDir ./star_index --genomeFastaFiles rDNA_sequence.fasta --genomeSAindexNbases 3
+
+#run STAR for the trimmed reads
+STAR --genomeDir ./star_index --readFilesIn ./trimmed.fastq
+
+#generate the read count matrix using featureCounts
+featureCounts -a rDNA.gtf -t CDS -o counts.txt Aligned.out.sam
+
+
+
+

intro-rna-seq/all_steps_wynton.sh

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+#!/bin/bash
+
+#This script should be run on the dev3 node of the UCSF Wynton HPC cluster
+#before running this script, do the following
+##  1. transfer the workshop files from your local computer to your wynton account
+##     {local}$ scp -r Downloads/Intro_to_RNA-seq_data_analysis/ alice@dt2.wynton.ucsf.edu:~
+##  2. create the singularity container rna_seq_container.sif on wynton using the below command
+##     [alice@log1 ~]$ singularity build rna_seq_container.sif docker://nfcore/rnaseq 
+
+cd ~/Intro_to_RNA-seq_data_analysis/
+
+singularity exec rna_seq_container.sif fastqc Bacteria_GATTACA_L001_R1_001.fastq
+
+singularity exec rna_seq_container.sif cutadapt \
+-a file:Adapter_Sequence.fasta \
+-o trimmed.fastq \
+Bacteria_GATTACA_L001_R1_001.fastq
+
+singularity exec rna_seq_container.sif fastqc trimmed.fastq
+
+singularity exec rna_seq_container.sif mkdir star_index
+
+singularity exec rna_seq_container.sif STAR \
+--runMode genomeGenerate \
+--genomeDir ./star_index \
+--genomeFastaFiles rDNA_sequence.fasta \
+--genomeSAindexNbases 3
+
+singularity exec rna_seq_container.sif STAR \
+--genomeDir ./star_index \
+--readFilesIn ./trimmed.fastq
+
+singularity exec rna_seq_container.sif featureCounts \
+-a rDNA.gtf \
+-t CDS \
+-o counts.txt \
+Aligned.out.sam

intro-rna-seq/steps_on_wynton_session1.txt

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+#Commands run on wynton in session 1 of the Intro to RNA-seq data analysis workshop
+
+#open a new terminal (MacOS) or command prompt (Windows) window 
+#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 ##############
+