Search Results for: RNAseq

12/21/2020 - Register Meeting number: 172 414 1612 Meeting Password: AmWdZgu*775 Please see information below about the upcoming SS/SC Brown Bag Seminar on next Monday December 21, 2020. Slides are already available on our website https://ccrod.cancer.gov/confluence/ Read More...

12/07/2020 - Register

07/23/2019 - https://cbiit.webex.com/recordingservice/sites/cbiit/recording/96b9adfc1c8645219a9772a601951732/playback

Here are a pair of examples of RNASEQ complete workflows RNASEQ Pipeline from NCI CCBR https://github.com/CCBR/Pipeliner/blob/master/RNASeqDocumentation.pdf RNASEQ Nextflow Pipeline from nf-core https://nf-co.re/rnaseq

RNASEQ looks at steady state mRNA levels which is the sum of transcription and degradation Protein levels are assumed to be driven by mRNA levels RNASEQ can measure relative abundance not absolute abundance RNASEQ is Read More...

There are data sets available in R to practice with or showcase different packages. For today's lesson and the remainder of this course, we will use data from the Bioconductor package airway to showcase Read More...

An example of a counts matrix for RNASEQ data.

This page contains content taken directly from the Biostars Handbook by Istvan Albert. Remember to activate the bioinformatics environment. conda activate bioinfo Install the statistical packages we will need for the analysis, curl http://data. Read More...

Follow the directions to install DESeq: DESeq To install these packages, start R (version "4.0") by typing "R" at the command line and enter: You will know you are in R when Read More...

Where is the RNA sequencing data that we will be using for this course? Remember we will be demonstrating the steps of RNA sequencing in class using the Human Brain Reference (HBR) and Universal Human Read More...

mkdir rnaseq cd rnaseq curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz | tar zxv Directories: * "reads" contains the sequencing reads * "refs" contains genome and annotation information using Read More...

mkdir rnaseq cd rnaseq curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz | tar zxv Directories: * "reads" contains the sequencing reads * "refs" contains genome and annotation information using Read More...

mkdir rnaseq cd rnaseq curl -s http://data.biostarhandbook.com/rnaseq/projects/griffith/griffith-data.tar.gz | tar zxv Directories: * "reads" contains the sequencing reads * "refs" contains genome and annotation information using Read More...

For this exercise, go back to the ~/biostar_class/hcc1395 folder and create a new directory called trimmed_data. {{Sdet}} Solution{{Esum}} cd ~/biostar_class/hcc1395 mkdir trimmed_data cd trimmed_data {{Edet}} The adapters Read More...

pros and cons https://alexslemonade.github.io/refinebio-examples/03-rnaseq/pathway-analysis_rnaseq_01_ora.html Where to find tools?

Quantitation Counting as a measure of Expression Most RNASEQ techniques deal with count data. The reads are mapped to a reference and the number of reads mapped to each gene/transcript is counted Read counts Read More...

Because of its vast dynamic ranges RNASEQ data is typically log transformed in order to: provide better visualizations and to present analysis software with a more "normal distribution".

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 following sources inspired this content: https://www.sc-best-practices.org https://hbctraining.github.io/scRNA-seq_online/ https://bioconductor.org/books/3.15/OSCA.basic/ This is only a small subset of tools available to single cell RNASeq. Read More...

Single cell RNASeq is a remarkably powerful tool for analyzing populations of cells that can be recovered from various experiments. Clustering and cell type annotation can be used to distinguish different populations with a level Read More...

We can use the airway package to see how this container works, including how to access and subset the data. What is the airway package? There are data sets available in R to practice with Read More...

The provided data set is an example of a real count matrix returned from the NCI CCR Sequencing Facility (CCR-SF). The provided file ( ./data/SF_example_RNASeq_1.txt ) contains RNAseq data for two sets of Read More...

Get the reads from http://data.biostarhandbook.com/books/rnaseq/data/golden.reads.tar.gz . You will also need to unpack the file. {{Sdet}} Solution{{Esum}} wget -nc http://data.biostarhandbook.com/books/rnaseq/data/ Read More...

Data Analysis Here are a pair of examples of RNASEQ complete workflows RNASEQ Pipeline from NCI CCBR https://github.com/CCBR/Pipeliner/blob/master/RNASeqDocumentation.pdf RNASEQ Nextflow Pipeline from nf-core https://nf-co.re/rnaseq Read More...

The Golden Snidget reference genome is located at http://data.biostarhandbook.com/books/rnaseq/data/golden.genome.tar.gz. Can you download and extract? {{Sdet}} Solution{{Esum}} Download wget http://data.biostarhandbook.com/books/rnaseq/ Read More...

Here are a number of visual elements that are typically produce from RNASEQ data. Normalization plots PCA and Volcano plots Scatter plot and correlation coefficients Heat Maps IGV Traces Resources

Lesson 7 Practice In Lesson 7, you learned how to download and work with archived and compressed files. To practice what you have learned, we will use the ERCC spike in control data, which Istvan Albert, creator Read More...

To add to the mRNA mapping problem is the existance of alternate splicing events. Attempting to identify alternate splicing in RNASEQ data is not something for the novice to attempt! .... get professional help

RNA-seqlopedia - https://rnaseq.uoregon.edu/ RNA-Seq by Example - https://www.biostarhandbook.com/

Visualization Here are a number of visual elements that are typically produce from RNASEQ data. Normalization plots PCA and Volcano plots Scatter plot and correlation coefficients Heat Maps IGV Traces Resources

A good experimental design is vital for the success of any RNASEQ experiment. Before you begin the experiment make sure you have a clear understanding of the technique and how to avoid costly mistakes that Read More...

30 minutes: Review 30 minutes: Downloading and organizing files for RNASeq files file compression and data set introduction setting up project folders Help session: Coding scavenger hunt

Now, grab the reference files from http://data.biostarhandbook.com/books/rnaseq/data/golden.genome.tar.gz . This time try out wget . If you aren't sure how to use wget , how might you find Read More...

By far the most popular platforms for RNASEQ experiments are the Illumina family of sequencers. All are Sequencing by Synthesis (SbS) and produce Short read lengths (50 to 300 bp). Consult with the Sequencing Core as to Read More...

This data set is from the Griffith lab RNA sequencing tutorial and are kept at http://genomedata.org/rnaseq-tutorial/practical.tar. This dataset is derived from a study that profiled the transcriptome of HCC1395 breast Read More...

Technical Replicates It’s generally accepted that they are not necessary because of the low technical variation in RNASeq experiments Biological Replicates (Always useful) Not strictly needed for the identification of novel transcripts and transcriptome Read More...

What tool(s) are available to assess quality of our raw sequencing data {{Sdet}} Answer{{Esum}} FASTQC will generate quality assessment reports for each FASTQ file separately (ie. if you have 12 files, 12 separate FASTQC reports Read More...

We will analyze these data by doing: 1. Alignment (hisat2) 2. Quantification (featureCounts) 3. Differential expression (DESeq) Use of a spike-in control Using a spike-in allows us to determine how well we can measure and reproduce data with Read More...

We will analyze these data by doing: 1. Alignment (hisat2) 2. Quantification (featureCounts) 3. Differential expression (DESeq) Use of a spike-in control Using a spike-in allows us to determine how well we can measure and reproduce data with Read More...

We will analyze these data by doing: 1. Alignment (hisat2) 2. Quantification (featureCounts) 3. Differential expression (DESeq) Use of a spike-in control Using a spike-in allows us to determine how well we can measure and reproduce data with Read More...

Basic RNASEQ Quality Control (QC) examines the technical characteristics of the data produced by the sequencer. ( It tells us nothing about whether the experiment worked . It answer the questions: Is the data of sufficiently high Read More...

We are going to download some bulk RNA-Seq test data and learn how to decompress it. First we will create a place to store the data. Go to the directory you've created for working Read More...

RNA-SEQ Overview What is RNASEQ ? RNA-Seq (RNA sequencing), uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment. (Wikipedia) Strictly speaking this could be any Read More...

The rapid advancement of single-cell technology has provided new powerful tools to answer many biological questions, such as identifying new or rare cell populations and characterizing the complexities of tumor heterogeneity. Realizing the great potential Read More...

This is part II of the article highlighting nf-core pipelines and specifically addresses the use of these pipelines in the DNAnexus cloud environment. Part I of the article can be found in the October 2023 topic Read More...

03/12/2025 - Clustering is one of the fundamental unsupervised machine learning algorithms. It is often used to group quantitative proteomic or RNAseq expression data to suggest sub-types of a particular cancer. This presentation covers building a Read More...

Differential expression analysis is the process of identifying genes that have a significant difference in expression between two or more groups. For many sequencing experiments, regardless of methodology, differential analysis lays the foundation of the Read More...

One particular critique of differential expression in single cell RNASeq analysis is p-value "inflation," where the p-values get so small that there are far too many genes exist with p-values below 0.05, even after Read More...

05/16/2024 - Qiagen CLC Genomics Workbench is a point-and-click bioinformatics software that runs on a personal computer and enables bulk RNA sequencing, ChIP sequencing, long reads, and variant analysis. NCI scientists can use CLC Genomics Workbench Read More...

04/26/2024 - Dear Colleagues,    In this webinar, you'll get an introduction to WebMeV. WebMeV aims to democratize bioinformatics analysis for biological sciences researchers.   The maturation of many bioinformatics processes Read More...

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . We are going to use the filtlowabund_scaledcounts_airways.txt file Read More...

Tidy data implies that we have one observation per row and one variable per column. This generally means data is in a long format. However, whether data is tidy or not will depend on what Read More...

Lesson 2 Exercise Questions: Part 1 (BaseR subsetting and Factors) The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . We are going Read More...

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . We are going to use the filtlowabund_scaledcounts_airways.txt file Read More...

Lesson 3 Exercise Questions: BaseR dataframe manipulation and factors The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . We are going Read More...

Tidy data implies that we have one observation per row and one variable per column. This generally means data is in a long format. However, whether data is tidy or not will depend on what Read More...

Let's learn how to further work with vectors, including creating, sub-setting, modifying, and saving. #Some possible RNASeq data cell_line

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of class here . The diffexp_ Read More...

Lesson 5 Exercise Questions: Tidyverse The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of Read More...

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of class here . The diffexp_ Read More...

Lesson 2 Exercise Questions: Part 2 (Tidyverse) The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside Read More...

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of class here . The diffexp_ Read More...

Lesson 4 Exercise Questions: Tidyverse The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of Read More...

Many of the packages that handle RNASeq count data do not work correctly with decimal numbers. We need to convert these numbers to integers using mutate() . Save your transformed data frame to an object named Read More...

In tab delimited files, data columns are separated by tabs. To import tab-delimited files there are several options. There are base R functions such as read.delim() and read.table() as well as the readr Read More...

In lesson 3, we learned how to read and save excel spreadsheet data to a R object using the tidyverse package readxl . Today we will use some example data from an excel spreadsheet to learn the Read More...

09/20/2023 - This session of the BTEP Coding Club will focus on the tool rMATS for differential alternative splicing event detection from RNA-Seq data. This 1-hour demo will provide a detailed overview of rMATS including why Read More...

Most RNASEQ techniques deal with count data. The reads are mapped to a reference and the number of reads mapped to each gene/transcript is counted Read counts are roughly proportional to gene-length and abundance Read More...

Lesson 12 Practice Objectives In this practice session, we will work with something new, which is a dataset from the Griffith lab RNA sequencing tutorial. Here, we will have a chance to practice what we have Read More...

Let's download the data and learn how to decompress it. First, we will create a place to store the data. Go to the directory you created for working with class material. If you haven' Read More...

Lesson 9 Practice Objectives In this practice session, we will apply our knowledge to learn about the reference genome and annotation file for the Golden Snidget dataset visualize the Golden Snidget genome using the Integrative Genome Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. 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...

Generating the Data General Rules for Sample Preparation Ignoring these simple guidelines will greatly increase the chances that your data will be unanalysable and/or your experiment unpublishable. Prepare all samples at the same time Read More...

Here, let's download the HBR and UHR dataset to get acquainted with it. First, we will use pwd to make sure we are in the home directory. pwd If we are in the home Read More...

Here, let's download the HBR and UHR dataset to get acquainted with it. First, we will use pwd to make sure we are in the home directory. pwd If we are in the home Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

Retrieve R "helper" scripts developed for Biostars environment. curl -O http://data.biostarhandbook.com/rnaseq/code/deseq1.r curl -O http://data.biostarhandbook.com/rnaseq/code/deseq2.r curl -O http://data.biostarhandbook. Read More...

NISC’s role within NHGRI, and more broadly across NIH, aims to advance genome sequencing and its many applications, with a goal not simply to produce sequence data, but to produce the infrastructure required to Read More...

The CCR Genomics Core is located in Building 41 on the NIH Bethesda campus. The primary goal of the Core is to provide investigators from CCR/NCI and other NIH Institutes access to genomic technologies and Read More...

nf-core is a community effort to generate a curated set of standardized, best-practice, reproducible, documented, NGS analysis pipelines. All these workflows are built using the versatile workflow manager, Nextflow , and have been released under the 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...

1. Introduction and Learning Objectives This tutorial has been designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples that Read More...

The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of class here . The diffexp_ Read More...

Lesson 4 Exercise Questions: Tidyverse The filtlowabund_scaledcounts_airways.txt includes normalized and non-normalized transcript count data from an RNAseq experiment. You can read more about the experiment here . You can obtain the data outside of Read More...

Learning Objectives Learn about data structures including factors, lists, data frames, and matrices. Load, explore, and access data in a tabular format (data frames) Learn to write out (export) data from the R environment Data Read More...

Objectives To understand some of the most basic features of the R language including: Creating R objects and understanding object types Using mathematical operations Using comparison operators Creating, subsetting, and modifying vectors By the end Read More...

In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...

In this lesson, attendees will learn how to transform, summarize, and reshape data using functions from the tidyverse. Learning Objectives Continue to wrangle data using tidyverse functionality. To this end, you should understand: how to Read More...

The object class used by the DESeq2 package to store the read counts and the intermediate estimated quantities during statistical analysis is the DESeqDataSet. --- Analyzing RNA-seq data with DESeq2 Constructing this object from a Read More...

Objectives Review important data wrangling functions Put our wrangling skills to use on a realistic RNA-Seq data set Data Wrangling Review Important functions by topic Importing / Exporting Data Importing and exporting data into the R Read More...

Objectives To explore Bioconductor, a repository for R packages related to biological data analysis. To better understand S4 objects as they relate to the Bioconductor core infrastructure. To learn more about a popular Bioconductor S4 Read More...

Data import and reshape Objectives 1. Learn to import multiple data types 2. Data reshape with tidyr : pivot_longer() , pivot_wider() , separate() , and unite() Installing and loading packages So far we have only worked with objects that Read More...

Introduction to ggplot2 Objectives Learn the ggplot2 syntax. Build a ggplot2 general template. By the end of the course, students should be able to create simple, pretty, and effective figures. Data Visualization in the tidyverse Read More...