Search Results for: Nano-DSC

05/03/2021 - Register/Join In the May NCI Imaging and Informatics Community Webinar, Dr. Chad Quarles will highlight how the improved understanding of the biophysics of contrast mechanism underlying dynamic susceptibility contrast (DSC) MRI is informing Read More...

After you are done editing, what is are the steps to exiting nano and returning to the prompt? {{Sdet}}{{Ssum}}Solution{{Esum}} Hit control x If you made edits, nano will ask if you like Read More...

nano design.csv Copy the text below to the nano editor, hit control-x and save to return to the terminal. sample,condition BORED_1.bam,BORED BORED_2.bam,BORED BORED_3.bam,BORED EXCITED_1.bam,EXCITED EXCITED_2. Read More...

What is the first step to editing a new or an existing file using nano. {{Sdet}}{{Ssum}}Solution{{Esum}} If you are editing a new file, then the command below will open a blank editor Read More...

Nano is a basic file editor that is built into Unix and enables editing of plain text files including txt, csv, fasta, genbank, gtf, and fastq. To edit a file using Nano, just use nano Read More...

Nano is a basic file editor that is built into Unix and enables editing of plain text files including txt, csv, fasta, genbank, gtf, and fastq. To edit a file using Nano, just use nano Read More...

nano (to open the nano editor to edit files) sbatch (to submit jobs to Biowulf) squeue (to check job status) scancel (to cancel jobs) scp (to copy content between local computer and Biowulf)

On Biowulf, create the file /home/$USER/bin/R with the following content: mkdir ~/bin nano ~/bin/R Paste the following into nano: #! /bin/bash module load R/4.2 exec R "$@" Make /home/$USER/ Read More...

The exercises below will further help you develop proficiency in using the Unix nano editor. You will modify the script we used in the lesson to download and assess the quality of sequencing data for Read More...

We need to make a few edits to SRR1553423_fastqc.sh before we can submit it as a batch job. Open the script with nano and make the necessary edits. {{Sdet}}{{Ssum}}Solution{{Esum}} nano Read More...

Submit a swarm script (name it SRP475677.swarm) to download the first 1000 sequences for the following accessions from SRA. Paired end mode was used. SRR27044727 SRR27044728 SRR27044729 SRR27044733 SRR27044734 {{Sdet}}{{Ssum}}Solution{{Esum}} nano SRP475677. Read More...

For this exercise, change back into the data directory. cd /data/username Make a directory called text_files_and_tabular_data. mkdir text_files_and_tabular_data cd text_files_and_tabular_data The touch Read More...

2024 Date: Tuesday, October 15, 2024 Time and Location: 11 am EST, ZOOM (INVITATION BY LMIG LIST SERVER) Speaker: Dr. Diego Presman (U Buenos Aires) Title: “Insights on Glucocorticoid Receptor Activity Through Live Cell Imaging” Summary: Eucaryotic transcription factors ( Read More...

pwd (print working directory) ls (list) nano (basic editor for creating small text files) rm (remove files) mkdir (make a directory) cd (change directory) mv (rename or move files) less (view files) man (manual) cp ( Read More...

Create the design.csv file using the nano editor. Recall that the design files contain nothing more than a column with sample names and a column informing of sample treatment condition. Some of the R Read More...

Create fastqc.swarm file with text editor (nano). fastqc -o output SRR10314042.fastq fastqc -o output SRR10314049.fastq fastqc -o output SRR10314054.fastq fastqc -o output SRR10314097.fastq fastqc -o output SRR10314043.fastq fastqc -o Read More...

Next, we need to generate the counts (ie. number of reads that map to a transcript). But first, change back into the ~/biostar_class/snidget folder and then take a moment to think about how Read More...

Swarm is a script for running a group of commands on Biowulf. Swarm reads a list of command lines and automatically submits them to the system. To create a swarm file, you can use " Read More...

Swarm is a script for running a group of commands on Biowulf. Swarm reads a list of command lines and automatically submits them to the system. To create a swarm file, you can use " Read More...

pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

To retrieve all the files at once, you can create a swarm job. nano set.swarm Inside the swarm file type #SWARM --threads-per-process 3 #SWARM --gb-per-process 1 #SWARM --gres=lscratch:10 #SWARM --module sratoolkit fasterq-dump -t /lscratch/$SLURM_ Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the "rm" command to remove files. Be careful! mkdir (make a directory) and Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the "rm" command to remove files. Be careful! mkdir (make a directory) and Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

Swarm is for running a group of commands (job array) on Biowulf. swarm reads a list of command lines and automatically submits them to the system as sub jobs. To create a swarm file, you Read More...

Let's go back to the biostar_class directory and create a folder called practice_trimming for this exercise. How do we do this? {{Sdet}} Solution{{Esum}} This depends on where you are currently (ie. Read More...

Let's submit a batch job. We are going to download data from the Sequence Read Archive (SRA) , a public repository of high throughput, short read sequencing data. We will discuss the SRA a bit Read More...

Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...

Getting VsCode to work interactively with R Step 1: Creating an ssh key to use VSCode Setup VSCode to run on a compute node using instructions outlined here . Step 2: ssh to Biowulf and start an interactive Read More...

Each version of R loaded as a module includes a number of installed packages . However, you may want to install additional packages, which will by default be stored in " ~/R/%v/library where %v Read More...

The final exercise in this lesson is to sort. To do this create text file called sorting_example.txt in the data directory. cd /data/username nano -L sorting_example.csv Then enter the following. Read More...

After this lesson, participants will Be able to describe shell and swarm scripts Use the Nano editor to edit scripts Submit shell and swarm scripts to the Biowulf batch system

After this lesson, participants should be able to Find bioinformatics applications that are installed on Biowulf Load applications that are installed on Biowulf Describe the Biowulf batch system Use nano to edit files Use swarm Read More...

After this lesson, participants should be able to Find bioinformatics applications that are installed on Biowulf Load applications that are installed on Biowulf Describe the Biowulf batch system Use nano to edit files Use swarm Read More...

module avail: list available applications on Biowulf module spider: list available applications on Biowulf module what is: get application description module load: load an application nano: open the Unix text editor to edit files touch: Read More...

module avail: list available applications on Biowulf module spider: list available applications on Biowulf module what is: get application description module load: load an application nano: open the Unix text editor to edit files touch: Read More...

How can the shell script in Question 3 be changed to obtain FASTQC results? {{Sdet}}{{Ssum}}Solution{{Esum}} nano SRP475677_fastqc.sh #!/bin/bash #SBATCH --job-name=SRP475677_fastqc #SBATCH --mail-type=ALL #SBATCH --mail-user=username@nih.gov # Read More...

ls (list) pwd (print working directory) touch (creates an empty file) nano (basic editor for creating small text files) using the "rm" command to remove files. Be careful! mkdir (make a directory) and Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

Navigating the NCBI website can be challenging. From a user perspective, nothing is as straight forward as you would expect. For the sequence read archive (SRA), there are fortunately some options. There are the convuluted Read More...

Most jobs on Biowulf should be run as batch jobs using the "sbatch" command. $ sbatch yourscript.sh Where yourscript.sh is a shell script containing the job commands including input, output, cpus-per-task, and Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Lesson 11 Practice Objectives In this lesson, we learned to merge multiple FASTQC reports into one perform data cleanup (quality and adapter trimming) to prepare our sequencing reads for downstream analysis. Here, we will put what Read More...

pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove files. Be careful! mkdir (make a directory) and rmdir (remove Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Let's use the tool Trimmomatic to clean up the adapters and the poor quality reads for SRR1553606. For help with Trimmomatic type trimmomatic --help at the command line. Before getting started with using trimmomatic, Read More...

GNU parallel executes commands in "parallel", one for each CPU core on your system. It can serve as a nice replacement of the for loop . See Tool: Gnu Parallel - Parallelize Serial Command Read More...

There are instructions for running SRA-Toolkit on Biowulf here ([https://hpc.nih.gov/apps/sratoolkit.html])(https://hpc.nih.gov/apps/sratoolkit.html). To start with, we will start up an interactive node using the & Read More...

Lesson 16 Practice Objectives In this lesson, we learned about the classification based approach for RNA sequencing analysis. In this approach, we are aligning our raw sequencing reads to a reference transcriptome rather than a genome. Read More...

The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command line. Begin Read More...

Lesson 2 Practice The instructions that follow were designed to test the skills you learned in Lesson 2. Thus, the primary focus will be navigating directories and manipulating files. Let's navigate our files using the command Read More...

The grep utility is used to search files looking for a pattern match. It is used like this. grep pattern options filename As our first example we will look for restriction enzyme (EcoRI) sites in Read More...

Now that we have accession numbers to work with, let's use parallel and fastq-dump to download the data. GNU parallel executes commands in "parallel", one for each CPU core on your system. Read More...

Lesson 5: Working on Biowulf Lesson 4 Review Flags and command options Wildcards ( * ) Tab complete Accessing user history with the "up" and "down" arrows cat , head , and tail Working with file content (input, Read More...

Lesson 2: Navigating file systems with Unix Quick review Unix is an operating system We use a unix shell (typically bash) to run many bioinformatics programs We need to learn unix to use non-GUI based tools Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn * What are sequence adapters? * Do we need to trim them before alignment? * How can I trim with a new adapter sequence? Be Read More...

How to download data from the Sequence Read Archive (NCBI/SRA) to your account on NIH HPC Biowulf You will need: active, unlocked Biowulf account (hpc.nih.gov) active Globus account for transferring files OR Read More...

touch creates an empty file nano basic editor for creating small text files rm remove files or directories. Be careful! mkdir make a directory and rmdir (remove a directory with NO files) mv rename or Read More...

First, let's set up our renv cache location. renv uses a global cache to reduce duplicate installs of packages across projects. When using renv with the global package cache, the project library is instead Read More...

We will create and submit a job script using sbatch that will run the R scripts in the project we created in Lesson 3 ( MyNewProject ). Example job script: nano rjob.sh Paste the following: #!/bin/bash # Read More...

Now that we have renv set up with our project, let's also establish a project structure. Let's exit R and edit our .Rprofile . Note When we ran renv::init() a local .Rprofile file Read More...

Submit a shell script (name it SRP475677.sh) to run seqkit stats for the FASTQ files that were just downloaded. {{Sdet}}{{Ssum}}Solution{{Esum}} nano SRP475677.sh #!/bin/bash #SBATCH --job-name=SRP475677_stats #SBATCH --mail-type= Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

In Biowulf, a swarm script can help with parallelization of tasks such as downloading multiple sequencing data files from the NCBI SRA study Zaire ebolavirus sample sequencing from the 2014 outbreak in Sierra Leone, West Africa Read More...

ssh (connect to remote computer such as a high performance computing cluster) pwd (print working directory) cd (change directory) ls (list directory content) mkdir (make a directory) and rmdir (remove a directory, must be empty Read More...

ssh (connect to remote computer such as a high performance computing cluster) pwd (print working directory) cd (change directory) ls (list directory content) mkdir (make a directory) touch (creates an empty file) nano (basic editor Read More...

For this portion of the class, change back to the /data/username folder cd /data/username Then make a new directory called SRP045416 and change into it. mkdir SRP045416 cd SRP045416 In Biowulf, a swarm Read More...

For this portion of the class, change back to the /data/username folder cd /data/username Then make a new directory called SRP045416 and change into it. mkdir SRP045416 cd SRP045416 In Biowulf, a swarm Read More...

2016-2024 Publications using images obtained in OMC

2024 Coutinho, L. L., Femino, E. L., Gonzalez, A. L., Moffat, R. L., Heinz, W. F., Cheng, R. Y. S., Lockett, S. J., Rangel, M. C., Ridnour, L. A. & Wink, D. A. NOS2 and Read More...

Lesson 2: Getting Started with QIIME2 Lesson Objectives Obtain sequence data and sample metadata Import data and metadata Discuss other useful QIIME2 features including view QIIME2, provenance tracking, and the QIIME2 forum. DNAnexus DNAnexus provides a Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Let's align an RNA-Seq sample using the "splice aware" aligner hisat2. First we will need to create the indices. Use this format: hisat2-build REFERENCE_GENOME INDEX_PREFIX Like this: hisat2-build Read More...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

Getting Started with Biowulf Biowulf is the NIH high performance computing cluster. It is a linux computing cluster with greater than 105,000 processors. The NIH HPC systems also house "hundreds of scientific programs, packages and Read More...

Lesson 6: Downloading data from the SRA For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch Read More...

Lesson 11: Merging FASTQ quality reports and data cleanup Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 10 Review In the previous lesson, we learned about the structure of the FASTQ Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

More useful Unix Flags and command options - making programs do what they do Use of wildcards Using tab complete for less typing Access your history with the "up" and "down" Read More...

Lesson 7: Downloading the RNA-Seq Data and Dataset Overview Lesson Review pwd (print working directory) ls (list) touch (creates an empty file) nano (basic editor for creating small text files) using the rm command to remove Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learning objectives: 1. Understand what a sequence alignment is and how different algorithms can effect alignments. 2. Learn how scoring matrices and gap penalties (gap Read More...

Lesson 4: Useful Unix For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 3 Review Biowulf is the high performance computing cluster at NIH. When you apply for a Biowulf account Read More...

Lesson 6: sra-tools, e-utilities, and parallel This page uses some content directly from the Biostar Handbook by Istvan Albert. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch or swarm Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page contains content taken directly from the Biostar Handbook (Istvan Albert). Always remember to activate the class bioinformatics environment. conda activate bioinfo For this data analysis, we will be using: Two commercially available RNA Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Obtain RNA-seq test data. The test data consists of two commercially available RNA samples: Universal Human Reference (UHR) and Human Brain Reference (HBR) . Read More...

Lesson 2: Getting Started with R on Biowulf Learning objectives Understand how R can be deployed on Biowulf Understand how to access and use R modules Learn to create a custom R library on Biowulf Deploying Read More...

Lesson 3: R Project Management and renv Learning objectives Discuss the importance of reproducibility Learn ways to make R analyses more reproducible Learn how to set up and organize an R project Learn how to use Read More...

Lesson 4: Submitting R Scripts via command line Learning Objectives Learn how to use R with less interaction Learn how to deploy sbatch R jobs, and learn about alternatives such as swarm . Learn about R job Read More...

Lesson 1: Introduction to Biowulf, Unix, and R Learning Objectives Learn about why you may want to use R on Biowulf. Refresh Unix and R skills. This lesson will not be hands on. Why use R Read More...