Search Results for: nucleotide extraction

10/20/2020 - Participants will learn how to develop artificial intelligence (AI) applications using MATLAB, even if they do not have a formal background in machine and deep learning. The goal of this course is to introduce Read More...

Partek Genomics Suite (Partek) is a graphical user interface (GUI) based bioinformatics package. It hosts a range of work flows that allow for gene expression, epigenetic, and association analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{ Read More...

Geneious Prime is a graphical user interface (GUI) based bioinformatics package that contains a suite of tools for molecular biology and Next Generation Sequencing analysis. {{Sdet}}{{Ssum}}Listing of Analysis Functions{{Esum}} Classic Computational Molecular Read More...

An interactive heatmap of the percent composition of each nucleotide base (A,T,C,G) along the bases (horizontal axis) for each of the FASTQ files (vertical axis) is presented next. Hover over a tile Read More...

An interactive heatmap of the percent composition of each nucleotide base (A,T,C,G) along the bases (horizontal axis) for each of the FASTQ files (vertical axis) is presented next. Hover over a tile Read More...

The Genomics Technology Laboratory is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, data analysis, and information management tools, in support of CCR Investigators. The laboratory develops integrated Read More...

06/12/2024 - Join us for an engaging training session where we will examine the similarities and differences between machine learning and statistical differential gene expression (DGE) analysis using Qlucore Omics Explorer. Qlucore Omics Explorer is a Read More...

01/22/2024 - Dear Colleagues,    Optical Genome Maps (OGM) provide scaffolding information for large DNA molecules. In this talk, we describe the use of this technology for detecting structural variants and chaining them Read More...

The field has moved to denoising sequences rather than OTU clustering. In a denoising approach, the exact biological sequence is inferred and noise is removed from the dataset via error correction. This is generally done Read More...

Work on this if you choose to, at your own leisure, or if time permits. How would you confirm that there is a potential single nucleotide variant at position 50,768,105 on chromosome 22 for the hcc1395_normal_ Read More...

This page contains content directly from the Biostar Handbook by Istvan Albert. Always remember to activate your bioinformatics environment. conda activate bioinfo What is a sequence pattern? A sequence pattern is a sequence of bases Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Always remember to start the bioinformatics environment when working on Biostar class material. conda activate bioinfo Let's start by creating a directory Read More...

First we will obtain the SRA data from the biostar handbook web site curl http://data.biostarhandbook.com/sra/sra-runinfo-2019-01.tar.gz --output sra-runinfo-2019-01.tar.gz Now we can unpack the data. tar Read More...

RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. “Basic modules” quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while “RNA-seq Read More...

Why do we need a reference genome? {{Sdet}} Solution{{Esum}} The reference genome serves as a "known" that guides us in constructing the genome of the unknown from sequencing data. {{Edet}} What file Read More...

There should not be spaces in Unix file names or directories. Here is a good method to use: Use the underscore (_) where a space would go, like this, to name a directory containing RNA-Seq data. Read More...

07/27/2022 - Many recent studies highlighted the improved capability of long-read sequencing to detect structural variation in the human genome. For example, these technologies was also recently utilized to produce the first complete assembly of the Read More...

04/21/2021 - Register Description: MacVector is a sequence analysis application for macOS computers that provides users with a variety of tools and functions to simplify the analysis, manipulation, assembly, and documentation of DNA and protein sequences. Read More...

01/14/2021 - Registration: https://cbiit.webex.com/cbiit/onstage/g.php?MTID=e968a58127acdb59b961e2ef13865c7ad Description: This workshop will focus on the analysis of Next Generation Sequencing (NGS) data using the Read More...

08/20/2020 - Single nucleotide polymorphism (SNP) & Variation Suite (SVS) is an analytic tool created to empower researchers to perform complex analyses and visualizations on genomic and phenotypic data. Genome-Wide Association Studies (GWAS) continues to be Read More...

The next figure shows "Per base sequence content", which is essentially the sequence make up along the bases of reads in the FASTQ file. If a library is random, then the percent composition Read More...

CLC Genomics Workbench (Qiagen) is a graphical user interface (GUI) based bioinformatics software. It houses tools for molecular biology and Next Generation Sequencing (NGS) analysis (see Listing of Analysis Functions below). {{Sdet}}{{Ssum}}Listing of Read More...

The next figure shows "Per base sequence content", which is essentially the sequence make up along the bases of reads in the FASTQ file. If a library is random, then the percent composition Read More...

For this exercise, click on the chromosome selection drop down and choose "All". Then load normal_rep1.bam and tumor_rep1.bam to the tracks. Unlike the bigWig files, which shows pre-calculated coverage Read More...

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...

NanoString Technology The nCounter® Analysis System is an automated, multi-application, digital detection and counting system which directly profiles up to 800 molecules simultaneously from a single sample using a novel barcoding technology. Profile hundreds of mRNAs, Read More...

CLIA-Certified Technologies Offered: Fragment Analysis for Micro-satellite Instability Detection, Pharmacoscan Array for Pharmacogenomics, Mutation Detection for PCR and Sanger Sequencing, DNA extraction from whole blood, saliva, FFPE tissues, buccal swabs, nails, hair, PBMCs, buffy coats, Read More...

The Genomics Laboratory (formerly Laboratory of Molecular Technology) is an integrated, high-throughput molecular biology laboratory focusing on the development of genetics and genomics technologies, together with associated laboratory automation systems, data analysis, and information management Read More...

[embed]https://youtu.be/yTl1Q0D7aZ0[/embed] 10x Genomics' supports multiple cancer research areas from single nucleotide and structural variant detection to single cell whole transcriptome gene expression analysis of thousands of individual Read More...

The CLIA Molecular Diagnostics Laboratory (CMDL) provides an array of services for groups at the NIH Clinical Center, Fort Detrick, and Hood College, among others. They support cancer- and disease-related research by making Read More...

The mission of Human Brain Collection Core (HBCC) within the National Institute of Mental Health, Division of Intramural Programs (NIMH IRP) is to conduct and support research on brain and behavior, with the goal of Read More...

04/16/2025 - Updated Location: ATRF, Frederick MD, Main Auditorium What to bring:  Laptop capable of connecting to internet via NIH wifi For questions or to register, please contact Amy Stonelake ( amy.stonelake@nih.gov ) Read More...

04/15/2025 - What to bring:  Laptop capable of connecting to internet via NIH  wifi Are you looking to expand the reach of your sequencing to enable what long read technologies can provide?& Read More...

03/13/2025 - UCSC Xena showcases seminal cancer genomics datasets from The Cancer Genome Atlas (TCGA) and the Pan-Cancer Atlas, as well as the Genomic Data Commons, Pan-cancer Atlas of Whole Genomes, and the International Cancer Genome Read More...

Long read sequencing was recently named 2022’s method of the year by Nature Methods . Long read sequencing technologies, those that generate sequence reads with lengths of 10s of kilobases or longer have several advantages over Read More...

The Advanced Biomedical Computational Science (ABCS) group focuses on applications of bioinformatics, computational and data science, and artificial intelligence to support NCI researchers. ABCS provides: • Subject matter expertise in genomics, proteomics, and imaging. • Machine learning/ Read More...

Lesson 14 Practice Objectives Here, we will practice using the Integrative Genome Viewer (IGV) to visualize the hcc1395 RNA sequencing alignment results. About the data and launching IGV We were introduced to the hcc1395 RNA sequencing Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinfo environment. conda activate bioinfo Then create a new directory for files we will be working with today in Read More...

Now that we have downloaded the HBR and UHR dataset and know where analysis tools are, let's start learning about RNA sequencing, by first learning about our reference genome and annotation files. Let's Read More...

Which reference genome are we using in this IGV session to view the alignment results for samples hcc1395_normal_rep1 and hcc1395_tumor_rep2? On what chromosome are the sequencing data mapping to? {{Sdet}} Solution{{ Read More...

Compare the output from these commands: ls ls -S ls -lh ls -h (when used with -l option, prints file sizes in a human readable format with the unit suffixes: Byte, Kilobyte, Megabyte, Gigabyte, Terabyte. Read More...

This page uses context taken directly from the Biostar Handbook by Istvan Albert. Remember to activate the class bioinformatics environment. conda activate bioinfo Introduction to Genomic Variation Genomic variations are typically categorized into different classes Read More...

We will build a database out of all features of the 2014 Ebola genome under accession number KM233118. This data will go into a new directory named "db_2014". mkdir -p db_2014 # Get the 2014 Ebola 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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * cd * mkdir * curl * tar * cat * grep * wc * outputting data * piping data from one command to another * cut Learn: * du * pip * csvkit * datamash Read More...

Lesson 12: RNA sequencing review 1 Learning objectives Here, we will do a quick review of what we have learned about RNA sequencing in Lessons 8 through 11. Accessing the Biostar handbook The URL for the Biostar handbook is 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...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: FASTQC for assaying quality of sequence reads MultiQC for combining multiple FASTQC reports into one report Trimmomatic for removing sequence data based Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Learn: FASTQC for assaying quality of sequence reads MultiQC for combining multiple FASTQC reports into one report Trimmomatic for removing sequence data based Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment. conda activate bioinfo The jellyfish program is dependent on a program called "gcc" which is Read More...

Step 1 for generating bigWig files is to convert the BAM alignment results to a bedGraph file that contains coverage along genomic regions. Enchancing your vocabulary: BED file - this is also known as Browser Extensible Read More...

08/03/2023 - Identification of evolutionarily related DNA or protein sequences (homologs) is a crucial step in many biology workflows. For example, homologous sequences are used to infer relationships between organisms, understand how sequence changes affect observable Read More...

11/09/2022 - Over the past decade the importance of Structural Variation (SV) is becoming more obvious not just for population diversity but also with clear impacts in multiple diseases (e.g. Neurological) as well as cancer.  Read More...

05/01/2020 - BioCyc.org [1] is an extensive web portal containing 17,000 microbial genomes and associated metabolic pathways. BioCyc databases are created through a process that combines computational inferences with imported and curated data from multiple sources. The Read More...

10/26/2018 - Variant Analysis using Genomatix GeneGrid ** please bring laptop with Flash installed for the hands-on portion of this demo Susan M. Dombrowski, PhD and Peter Grant, Genomatix, Inc. Genomatix GeneGrid is a variant annotation and Read More...

04/25/2017 - This talk will be an introduction to Methyl-seq, where you will learn about leveraging the power of next-generation sequencing (NGS), both genome-wide and targeted approaches, that can provide insight into methylation patterns at a Read More...

05/16/2016 - This 2-day course, which includes both lecture and hands-on components, will teach the basic concepts and practical aspects of ChIP-Seq Data Analysis. There will also be a talk on ENCODE and a comprehensive discussion Read More...

03/08/2016 - BTEP Workshop on Exome-Seq Data Analysis and Variant Annotation (2-day) This workshop will cover the basics and best practices of exome-seq analysis including downstream interpretation of variants using a variety of in-house, open-source and Read More...

11/18/2014 - Day 1 - AM (9:30-12:30)  Introductory Lecture ( Peter FitzGerald, PhD - CCR, NCI ) Introduction Historical Perspective and Technical Variations Experimental methodology Comparison to ChIP-Chip Data Analysis Experimental Design Quality Control  Peak Calling (Different methodologies) Major Read More...

For this exercise, click on the chromosome selection drop down and choose "All". Then load normal_rep1.bam and tumor_rep1.bam to the tracks. Unlike the bigWig files, which shows pre-calculated coverage Read More...

There should not be spaces in Unix file names or directories. There are many strategies that can be used to avoid spaces in file names. Though, consistency is key. One good method is using snake_ Read More...

Change into the hcc1395_b4b folder in the participant's Biowulf /data directory. cd hcc1395_b4b Next, use ls with the -1 option to list the contents in the reads directory one item Read More...

Change into the hcc1395_b4b folder in the participant's Biowulf /data directory. cd hcc1395_b4b Next, use ls with the -1 option to list the contents in the reads directory one item Read More...

The reference genome is a completely assembled sequence that we can compare other sequences to. For high throughput sequencing, we need the known sequences so that we can find out where in the genome each Read More...

The reference genome is a completely assembled sequence (ie. the order in which the nucleotides are arranged is known). For high throughput sequencing, the known sequence help scientists find out where in the genome each Read More...

The reference genome is a completely assembled sequence (ie. the order in which the nucleotides are arranged is known). For high throughput sequencing, the known sequence help scientists find out where in the genome each Read More...

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...

The CCR Collaborative Bioinformatics Resource (CCBR) is a centrally funded resource group which provides a mechanism for CCR researchers to obtain many different types of bioinformatics assistance to further their research goals. The group has Read More...

The National Cancer Institute (NCI) is developing a national repository of Patient-Derived Models (PDMs) comprised of patient-derived xenografts (PDXs), patient-derived organoids (PDOrg), and in vitro patient-derived tumor cell cultures (PDCs) and cancer-associated fibroblasts (CAFs). These Read More...

The introduction of DNA sequencing instruments capable of producing millions of DNA sequence reads in a single run has profoundly altered the landscape of genetics and cancer biology. Complex questions can now be answered at Read More...

The computational chemistry and protein modeling team in the Advanced Biomedical Computational Science (ABCS) group provides novel solutions in structural modeling and computational chemistry. Computational scientists in the group collaborate with NCI researchers by using Read More...

Listed below are the video recordings of past BTEP events (classes, seminars, workshops). Videos are hosted on various servers and may play slightly differently. Some videos may be downloaded for local viewing. Recorded Videos of Read More...

Lesson 3: Creating a feature table Lesson Objectives Check for primers Generate an ASV count table and representative sequence file Understand the difference between OTU picking and denoising The two primary files that will be used Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

Lesson 9: Reference genomes and genome annotations used in RNA sequencing Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 8 Review In Lesson 8, we learned about the basics of RNA sequencing, Read More...

A search may take place in nucleotide space, protein space or translated spaces where nucleotides are translated into proteins. Searches may implement search “strategies”: optimizations to a specific task. Different search strategies will produce different Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment and create a directory for today's work. conda activate bioinfo mkdir blast cd blast What is 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...

Step 1 for generating bigWig files is to convert the BAM alignment results to a bedGraph (with extension bg) file that contains coverage along genomic regions. Enhancing your vocabulary: BED file - this is also known 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...

Alignment RNASeq Mapping Challenges The majority of mRNA derived from eukaryotes is the result of splicing together discontinuous exons, and this creates specific challenges for the alignment of RNASEQ data. Mapping Challenges Reads not perfect Read More...

We previously stored FASTQC results for the HBR and UHR raw sequencing data in the ~/biostar_class/hbr_uhr/QC directory (recall that ~ denotes home directory). So before getting started, change into this folder. cd ~/ Read More...

In lesson 9, we learned that reference genomes came in the form of FASTA files, which essentially store nucleotide sequences. In this lesson, we will learn about the FASTQ file, which is the file format that 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...

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...

Lesson 10: Introducing the FASTQ file and assessing sequencing data quality Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 9 Review In the previous lesson, we explored the reference genomes and 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...

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 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain 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...

Lesson 14: Visualizing alignment results Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 13 Review Previously, we used the application HISAT2 to align the raw sequencing data from the Human Brain 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...

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...

05/22/2017 - Driven by the decreasing costs and increasing performance of next-generation sequencing (NGS) technologies, the amount of available genomic data has grown exponentially in recent years.  While most of the analyses of these data is Read More...

No summary available.