Merge branch 'master' of https://github.com/gladstone-institutes/Bioinformatics-Workshops

intro-rna-seq/README.md

@@ -2,12 +2,13 @@
 [Link to wiki page](https://github.com/gladstone-institutes/Bioinformatics-Workshops/wiki/Introduction-to-RNA-Seq-Analysis)
 
 ### Description of files
-- Single_read.fastq (fastq file with a single read to understand the fastq file format)
+1. Single_read.fastq (fastq file with a single read to understand the fastq file format)
-- Bacteria_GATTACA_L001_R1_001.fastq (single-end small practice data with 100k reads for the demo in the workshop)
+2. Bacteria_GATTACA_L001_R1_001.fastq (single-end small practice data with 100k reads for the demo in the workshop)
-- Adapter_Sequence.fasta (fasta file with adapter sequence for demo with cutadapt)
+3. Adapter_Sequence.fasta (fasta file with adapter sequence for demo with cutadapt)
-- rDNA_sequence.fasta (fasta file with the reference genome sequence for demo with STAR aligner)
+4. rDNA_sequence.fasta (fasta file with the reference genome sequence for demo with STAR aligner)
-- rDNA.gtf (GTF file with the annotations for demo with featureCounts)
+5. rDNA.gtf (GTF file with the annotations for demo with featureCounts)
-- all_steps_wynton.sh (shell script for running all the analysis steps on UCSF Wynton  command-line interface using the practice data provided)
+6. all_steps_wynton.sh (shell script for running all the analysis steps on UCSF Wynton  command-line interface using the practice data provided)
-- steps_on_wynton_session1.txt (text file with steps used on wynton to download/uplaod files, change directories etc in session 1)
+7. steps_on_wynton_part1.txt (text file with steps used on wynton to setup the folders, upload the data and create a singularity container)
-- steps_on_wynton_session2.txt (text file with steps used on wynton to download/uplaod files, change directories etc in session 2)
+8. steps_on_wynton_part2.txt (text file with steps used on wynton to run the bulk RNA-seq analysis using the demo files)
-- all_steps_docker_desktop.sh (shell script for running all the analysis steps using Docker Desktop and the practice data provided)
+9. all_steps_docker_desktop_mac.sh (commands for running all the analysis steps using Docker Desktop and the demo files on MacOS)
+10. all_steps_docker_desktop_windows.sh (commands for running all the analysis steps using Docker Desktop and the demo files on Windows)

intro-rna-seq/all_steps_docker_desktop_mac.sh

@@ -0,0 +1,56 @@
+#!/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. Download the workshop materials at https://github.com/gladstone-institutes/Bioinformatics-Workshops/raw/master/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip?raw=true.
+##  3. Unzip the workshop materials in the Downloads folder
+##  4. Open a new terminal 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
+#change the path below to the path on your computer where the downloaded materials are unzipped
+##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 the downloaded materials folder
+#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
+
+
+# END #

intro-rna-seq/all_steps_docker_desktop_windows.sh

@@ -0,0 +1,60 @@
+#!/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
+##	   If Docker Desktop gives a pop-up that it requires a newer WSL kernel version, open a new command prompt window and run the below command:
+##	   $ wsl --update
+##	   Restart Docker Desktop
+##  2. Download the workshop materials at https://github.com/gladstone-institutes/Bioinformatics-Workshops/raw/master/intro-rna-seq/Intro_to_RNA-seq_data_analysis.zip?raw=true.
+##  3. Unzip the workshop materials in the Downloads folder
+##  4. Open a new command prompt window 
+
+##run the below commands in the command prompt 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
+#change the path below to the path on your computer where the downloaded materials are unzipped
+docker run --name rna_bash --rm -it -v C:\Users\ayushi.agrawal\Downloads\Intro_to_RNA-seq_data_analysis\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 the downloaded materials folder
+#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
+
+
+#STAR does not work on windows so, we will be using another aligner "HISAT2" for the demo
+#create a new folder
+mkdir hisat2_index
+
+#create the hisat2 index
+hisat2-build -p 7 rDNA_sequence.fasta hisat2_index/rDNA_
+
+#run hisat2 for the trimmed reads
+#HISAT2 and STAR are different aligners with different defaults, scoring algorithms, etc. This might result in different outputs from the two aligners. 
+hisat2 -p 7 -x hisat2_index/rDNA_ -U ./trimmed.fastq -S hisat2_aligned_out.sam
+
+#generate the read count matrix using featureCounts
+featureCounts -a rDNA.gtf -t CDS -o counts.txt hisat2_aligned_out.sam
+
+
+# END #

intro-rna-seq/steps_on_wynton_part1.txt

@@ -9,8 +9,8 @@
 #enter your wynton password when prompted and hit enter
 
 #once you are logged in to wynton,
-#list the contents of the home diretory or ~
+#list the contents of the home directory or ~
-#the uploaded folder Intro_to_RNA-seq_data_analysis shoudl appear in the result
+#the uploaded folder Intro_to_RNA-seq_data_analysis should appear in the result
 [alice@log2 ~]$ ls
 
 #login to the development node