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Bioinformatics
nano file2.txt Let's put something in this file. Unix is an operating system, just like Windows or MacOS. Linux is a Unix like operating system; sometimes the names are used interchangeably. Nano commands Read More...
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Bioinformatics
nano file2.txt Let's put something in this file. Unix is an operating system, just like Windows or MacOS. Linux is a Unix like operating system; sometimes the names are used interchangeably. Nano commands Read More...
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Bioinformatics
Nano is a built-in Unix text editor. We can use nano to create SRR1553606_fastqc.sh. The syntax here is nano file_to_edit so in this example do the following. nano SRR1553606_fastqc.sh Read More...
Bethesda, MD
Collaborative
The Spatial Imaging Technology Resource (formerly the Nanoscale Protein Analysis Section of the Collaborative Protein Technology Resource or CPTR) provides expertise and service in state-of-the-art protein analysis technologies to advance CCR research in basic discovery Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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)
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Bioinformatics
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...
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Bioinformatics
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...
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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...
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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...
Frederick, MD
Collaborative
NCI established the Nanotechnology Characterization Laboratory (NCL) to support the extramural research community to accelerate the progress of nanomedicine by providing preclinical characterization and safety testing of nanoparticles. It is a collaborative effort between NCI, Read More...
Frederick, Maryland
Core Facility
Repositories
The Biological Products Core provides the AIDS research community with high-quality purified preparations of various strains of Human Immunodeficiency Virus (HIV) and Simian Immunodeficiency Virus (SIV), economically prepared by leveraging the economy of scale. Materials Read More...
Frederick, MD
Collaborative
The Antibody Characterization Laboratory (ACL) is the laboratory responsible for the development of well-characterized monoclonal antibody reagents. The NCI’s Office of Cancer Clinical Proteomics Research funds ACL as a resource to the entire cancer Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
It may be useful to configure the text editor used by git (the default is vim). Today's instructor happens to prefer emacs: git config --global core.editor "emacs" Below is a list Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
Bethesda, MD
Core Facility
The Biophysics Core’s mission is to provide support in the study of macromolecular interactions, dynamics, and stability by offering consultations, training, professional collaborations, and instrument access. General Services: Multi-technique molecular interaction studies, Kinetic and Read More...
Bethesda, MD
Core Facility
The core provides access to several different state-of-the-art 3D microscopes as well as computers to visualize and process image data. The facility houses equipment for 2D or 3D imaging of fixed and living specimens. High Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
Web Page
Bioinformatics
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...
Web Page
Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
We can also take advantage of swarm for running jobs in parallel, as we did in the previous lesson. Note This should be run from Biowulf, not Helix. cd .. mkdir swarm cd swarm We can Read More...
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Bioinformatics
Directories are folders that can store files, other directories, links, executables, etc. The file system is hierarchical with the root directory (/) at the top. Commands useful for navigating our file system and handling files include: Read More...
Frederick, MD
Core Facility
The Clinical Support Laboratory offers processing, tracking, and testing of a broad range of clinical samples. Support can begin at the early stages of clinical trial development to aid in developing a comprehensive strategy for Read More...
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Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...
Frederick, MD
Core Facility
Protein Characterization Laboratory (PCL) offers various technologies to CCR investigators to characterize proteins and metabolites. The laboratory develops and applies state-of-the-art analytical technologies, primarily mass spectrometry, liquid chromatography, and Surface Plasmon Resonance (SPR), to advance Read More...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...
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Bioinformatics
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...