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May
6
Cambridge Healthtech Institute and Bio-IT World’s Inaugural
RNA-Seq and Transcriptome Analysis
Part of the Fifth International Clinical Genomics & Informatics Europe event
5-6 December 2013 | Sheraton Lisbon Hotel & Spa | Lisbon, Portugal
Transcriptome sequencing (RNA-Seq) is a robust approach steadily replacing microarrays as the choice method to accurately profile and quantify overall gene expression levels, while simultaneously allowing unbiased discovery of alternative splicing variants, rare and novel transcripts, miRNA precursors, differential isoforms and de novo analysis of samples. The ability to obtain a complete picture of disease transcriptomes provides clearer understanding of how the underlying genome is converted into the functional proteins, allowing for clinical utility in patient classification, diagnosis, and individualized treatment. However, a myriad of advanced bioinformatics tools and techniques for quality control, pre-processing, alignment, quantitative analysis and differential expression pose significant hurdles for many biologists and clinicians. Cambridge Healthtech Institute and Bio-IT World’s RNA-Seq and Transcriptome Analysis is designed to navigate the many bioinformatics challenges encountered by transcriptome sequencing, while highlighting its recent clinical applications. Read more
Incoming search terms:
- www rna-seqblog com rna-seq-and-transcriptome-analysis-conference
May
6
Workshop on RNA-Seq data analysis
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From Raw Sequence Data To mining Functional Information From Gene Lists Using Galaxy And R
The workshop is currently full. However, if there is enough demand we will offer it again. So if you are interested in attending, please fill in the information here. Also, people on the waiting list will receive the first opportunity to sign up for the next workshop!
Dates: June 3rd, 4th, 6th & 7th, 2013
Time: 1 pm – 5 pm
Location: 607 IGB – University of Illinois High-Performance Biological Computing
Workshop description: This is a 4-day workshop for RNA-Seq data analysis using the Galaxy interface and R. It will cover experimental design, evaluation of sequencing data, genome alignment, gene count extraction, statistical analysis to find differential expression and data mining. Data mining will include annotation of gene lists, Venn diagrams, heatmaps. The workshop will use the local Galaxy instance and open-source R and Bioconductor packages (no prior experience with Galaxy or R is necessary). Read more
Incoming search terms:
- cummerbund rna seq online
- miRNAs bioconductor
- pipeline for differential expression with galaxy
- R walpepar
- tophat bioconductor
- www rna-seqblog com workshop-on-rna-seq-data-analysis
May
3
RNA-Seq analysis using Galaxy
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- Event: RNA-Seq analysis using Galaxy
- Start: July 4, 2013 9:00 am
- End: July 4, 2013 5:30 pm
- Cost: $95 (morning only), $190 (full day)
- Category: Training
- Contact: QFAB Bioinformatics
- Phone: +61 7 3346 2095
- Email: m.crowe@qfab.org
- Venue: IHBI Seminar Room
- Address: QUT Kelvin Grove campus, 60 Musk Avenue, Kelvin Grove, QLD, 4059, Australia Google Map
Introduction
This hands-on workshop introduces the concepts of RNA-Seq analysis from data preparation through to statistical testing for differential gene expression (DGE). Using Galaxy, a platform that provides a user-friendly interface to bioinformatics tools, Mark Crowe from QFAB will introduce the tools, data types and workflow of DGE analysis.
An optional afternoon session will cover more advanced topics, including identification of novel transcript isoforms, generation of graphical output from RNA-Seq data, and analysis of data from non-model organisms, along with practice exercises.
Recommended participants: Biologists and bioinformaticians planning to work with RNA-Seq data for differential gene expression. Participants must bring their own laptops with wireless network capability.
Morning session
Basic RNA-Seq analysis and an introduction to Galaxy. Includes morning tea.
Full day
Morning session plus advanced topics and practice exercises. Includes morning and afternoon tea.
Incoming search terms:
- feedback opinions c1 fluidigm platfor
- galaxy rna seq coffea
- RNA seq analysis using Galaxy
- web administrator blog australia
- www rna-seqblog com rna-seq-analysis-using-galaxy
May
2
Genotype-Tissue Expression Project Community Meeting
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The goal of the first GTEx Project Community Meeting is to share information about the project and to showcase advances made during the project’s initial pilot phase. In addition to describing the project’s current status and goals during the upcoming scale up phase, the meeting will highlight the current pilot data set available including demonstrations of how and where to access the data, what data are available, current methodologies used, and what analyses can be done using the project portal.
Most of the meeting will be devoted to scientific presentations highlighting use of the current data set in analyses including estimates of gene expression variability, alternative splicing, and allele specific expression among individuals and tissues, discovery of shared and tissue specific eQTL’s, integration with ENCODE annotation, and network inference.
Meeting Agenda will be announced as oral presentations are finalized.
Registration is free but space is limited, so sign up today!
About the Genotype-Tissue Expression project
The Genotype-Tissue Expression project (GTEx) aims to create a public atlas of human gene expression and its regulation across multiple tissue types, enabling the research community to discover expression quantitative trait loci (eQTL) and help interpret associations with disease. While initial transcript data was generated using both arrays and RNA Seq to benchmark against one another, all data moving forward will be generated solely by RNA sequencing. By the end of the project we expect to have generated RNA sequence data from ~25,000 human tissues.
GTEx pilot data are now available at dbGaP and the GTEx Portal.
Incoming search terms:
- * seq download
- error=expect even number of files fusionmap seqanswers
- pjlnjcvlt
- POSTER PRESENTATION Open AccessEvaluation of bacterial ribosomal RNA (rRNA)depletion methods for sequencing microbialcommunity transcriptomes
- strengths weakness financial study rna-seq
- www rna-seqblog com genotype-tissue-expression-project-community-meeting
May
1
Introductory Course – The Power of RNA-seq
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General info
- Date - 05 Jun 2013 - 07 Jun 2013
- Location – Wageningen, the Netherlands
- Keywords – RNA-seq, transcriptome, experimental design, statistics, data analysis, mapping, quantification, differential expression, interpretation, pathways
- Organiser – Experimental Plant Sciences (EPS, Wageningen UR) & NBIC
- Teacher(s)
- Gabino Sanchez-Perez
- Edouard Severing
- Sandra Smit
- Ole Madsen
- Elio Schijlen
- Contact(s)
- Harm Nijveen
- Patrick Koks
- Sandra Smit
Description
The Power of RNA-seq is an introductory course for researchers who want to use RNA-seq in their research project.
The course will foc
us on questions like:
- Which questions can be addressed with RNA-seq?
- How many samples and replicates do I need?
- Which steps are involved in an RNA-seq experiment?
- What is Differential Expression?
- What can go wrong?
This is a 3-day course that will consist of lectures in the morning and extensive hands-on computer practicals in the afternoon. You’ll learn about all aspects of RNA-seq during the morning lectures on NGS & RNA-seq theory, but also the context, applicability, power and expected results of RNA-seq experiments. During the practicals, you’ll learn the basic steps an RNA-seq pipeline consist of, how to interpret your data and to put the results to use in your research project. We’ll use Galaxy, R and webtools for this.
topics:
- experiental design
- sequencing requirements
- steps in RNA-seq data analysis (data quality control, transcript identification, quantification, differential expression, interpretation)
target audience:
Researchers in Life Sciences (‘biologists’) starting with application of NextGen Sequencing & RNA-seq.
- No previous NGS experience is needed
- No command line or Linux computer experience is required
- No R-experience is required
For more information, contact Patrick Koks
Incoming search terms:
- Transcriptome seq
- RNAseq deduplication
- cuffdiff test statistics likelihood test
- Introductory Course – The Power of RNA-seq
- tomato genome size rnaseq
- differential expression and rna seq
- normalizing time course rna-seq
- tools available for differential expression
- RNA-seq is an effective method for studying the transcriptome
- rna-seq estimates varaince
May
1
Seminar – RNA-Seq for entomologists: addressing questions of sequencing depth and tissue specificity
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Dr.Brian Johnson, Department of Entomology & Nematology, UC Davis
Monday, May 6, 2013
4:10–5 p.m.
Location: Genomics Building 1102A
Parking Information
Category: Seminar
Description:
RNA-Seq is revolutionizing the study of gene expression. RNA-Seq has been shown to be quantitatively accurate over a larger range of expression levels than previous methods, such as microarrays, while also being more effective at identifying genes that show low expression levels. While the nuts and bolts of how best to use RNA-Seq are being addressed in a variety of contexts, major unresolved questions remain. With respect to insect studies, two questions of pressing concern are the sequencing depth necessary for documenting differential expression of genes of various classes, and the necessity, or lack thereof, of tissue specific RNA extractions. Here I will present results from two RNA-Seq studies exploring these issues. The primary results center on the utility of shallow RNA-Seq for many questions of interest to entomologists, and the necessity of tissue specificity for accurate quantification of gene expression. As extractions from body segments, and even whole insects, are common for insect RNA-Seq studies, the results are topical for those planning RNA-Seq studies.
Open to: Faculty/Staff Only
Admission: Free
Sponsor: Entomology Department
Contact Information:
Dr. Bradley White
951-827-2626
bradley.white@ucr.edu
Apr
12
Back from AACR
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Just returned from a great week at the American Association for Cancer Research (AACR) annual meeting and RNA-Seq was a big topic there. Saw some great presentations and posters describing the use of RNA sequencing as a powerful tool in the fight against a devastating disease. The exhibit hall was chock full of companies offering everything form library prep kits to sequencing services to data analysis software packages. There are companies providing all type of RNA sequecing services from microRNA to whole transcriptome sequencing.
You can find a list of the companies that exhibited at the conference at: http://www.aacr.org/Uploads/DocumentRepository/2013AM/exh_list.pdf
Does anyone who attended the conference have any comments on their experience?
Incoming search terms:
- concept talk quartz seq
- aacr poster ppt
- www rna-seqblog com back-from-aacr
Apr
9
Your comprehensive guide to applying RNA-Seq in research and drug discovery
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Attending RNA-Seq 2013 will arm you with the knowledge and skills you need to optimize the practical application of RNA-Seq technology in your lab.
Whether you’ve been using RNA-Seq for years and feel relatively well established, or it’s a totally new addition to your research programs, this agenda has been designed for you.
- Hear pioneering case studies on the most innovative applications of RNA-Seq so that you can return to the lab and put into operation immediately
- Discover how to cost-effectively manage the transition from microarray to RNA-Seq and ensure the hassle-free integration of technologies and data sets
- Leverage the latest advances in RNA-Seq technology for drug discovery and development by meeting with you’re the experts from universities, pharma and genome institutes
Enter the minds of the RNA-Seq experts from Bristol-Myers Squibb, Yale University, Merck, Genentech, Broad Institute, AstraZeneca, Stanford and a whole lot more. This is the perfect opportunity to hear novel approaches to overcoming the challenges preventing you from applying RNA-Seq to its full potential in the lab.
RNA-Seq 2013 brings together RNA-Seq leaders and innovators from pharma, biotech, genome institutes and universities. Leave the meeting with…
- An understanding of when and how to transition to RNA-Seq from microarray technology for maximum accuracy of gene expression measurement
- A toolbox of bioinformatics solutions and the most appropriate and unified integrated approach to managing, analyzing and interpreting huge volumes of data
- Knowledge of how an exceptional experimental design can help to enhance drug discovery to maximize the results
- An overview of the benefits of outsourcing to boost the time and cost efficiency of your NGS program for more streamlined applications
- An expert’s guide to the latest and best software frameworks for de novo transcriptome assembly and analysis
- The answers to optimizing biomarker discovery and target validation through streamlined techniques data application and integration techniques
Mar
26
You have until this Friday 29th March to register for RNA-Seq 2013 (18-20 June, Boston) at the best possible rates.
RNA-Seq 2013 brings together the latest knowledge and success stories for applying RNA-Seq technology in drug discovery and development.
The agenda is delivered by leading RNA-Seq experts from across industry and academia. Download the brochure for the full agenda and speaker line up.
Incoming search terms:
- www rna-seqblog com early-registration-closing-friday-rna-seq-2013
Mar
6
Bioinformatics courses, boot camps and workshops presented by the University of California, Davis Bioinformatics Core
RNA-seq has emerged as a standard tool to study transcriptomes through massively parallel sequencing. The ability to generate millions of cDNA sequences makes it possible to study novel organisms as well as model organisms with unprecedented sensitivity and reproducibility. In this bootcamp, we will introduce the basic concepts of RNA-Seq and illustrate data analysis workflows through lectures and hands-on activities, including best practices for quality control, read alignment, and expression analysis. Other topics will include experimental design and basic statistical analysis of unreplicated and replicated biological sample data, alignment browsers and high performance computing techniques for dealing with transcriptomic data. Participants will spend most of their time using the Galaxy platform to work through the most common RNA-Seq data analysis workflows. Prior experience with next generation sequences, or our Next Generation Sequencing Technology Fundamentals & Applications bootcamp, is highly recommended. It is also recommended that students have some prior experience with Galaxy, or have taken our Introduction to Galaxy bootcamp.
Incoming search terms:
- bioinformatics boot camp munich 2013
- referenced based transcriptome pathway analysis
- workshop rna seq 2013 munich
- www rna-seqblog com april-11-2013-boot-camp-introduction-to-rnaseq
Mar
5
3rd Annual RNA-Sequencing Conference – Special Offer to Blog Readers
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The RNA-Seq Blog has formed a partnership with CHI, and as a special offer to readers of the blog, CHI will offer you a partner discount – a savings of $200 off the current published rate.
CHI’s 3rd Annual RNA-Sequencing conference is only weeks away but there is still time to register and reserve your place.
RNA-Sequencing : Differential Expression in Depth conference is part of the 4th annual X-Gen Congress & Expo 2013
(http://www.xgencongress.com/RNA-Seq), March 18-20 in San Diego, CA.
X-Gen Congress is comprised of three scientific conferences
focused on RNA-Sequencing, DNA-Sequencing and Genomic Data Analysis. Your registration allows access to all three conferences.
Sessions Include:
- Functional Data Analysis
- Exome Sequencing
- Single-Cell Sequencing
- Advances in Clinical Research
- Nanopore Sequencing
And more . . . .
To take advantage of this offer, please enter code LNKR100 when registering.
To Register:
Call toll free: +1-888-999-6288
Visit: https://chidb.com/register/2013/xgn/reg.asp
Feb
25
Title – Analyzing Illumina RNA-seq Data with the CRI
Instructor - Elizabeth Bartom, PhD and Lei Huang, PhD
Location – Biological Sciences Learning Center – Room 018 (basement)
Date & Time – February 25, 2013 9am-12pm
Register - Register Here
RNA-seq is a revolutionary approach to transcriptome profiling that uses the next-generation sequencing technologies. It provides more accurate measurement of the expression levels of transcripts and their isoforms compared to other methods including microarrays. In this tutorial, we will learn to use the CRI’s RNA-Seq pipeline (available on brdfgate server, BIOS HPC cluster, and CRI Galaxy) to analyze Illumina RNA sequencing data. The analysis will be performed in four steps :
- Step 1: Assess the sequencing data quality using FastQC
- Step 2: Align the short reads to the human genome using Tophat
- Step 3: Analyze expression using Cufflinks
- Step 4: Collate results with in-house scripts
The Center for Research Informatics (CRI) provides computational resources and expertise in biomedical informatics for researchers in the Biological Sciences Division (BSD) of the University of Chicago. This workshop is part of a series of monthly training events focusing on using University of Chicago’s computational resources to analyze Next-Generation Sequencing and Microarray data.
As a bioinformatics core, we are actively improving our pipelines and expanding pipeline functions. The tutorials will be updated in a timely manner but may not reflect the newest updates of the pipelines. Stay tuned with us for the latest pipeline release.
If you have any questions, comments, or suggestions, feel free to contact our core at bioinformatics@bsd.uchicago.edu or one of our bioinformaticians.
Incoming search terms:
- advanced rna-seq analysis topics and trouble- shooting
- bioinformation rna-seq
- Lei Huang RNA-Seq
Feb
21
Your comprehensive guide to applying RNA-Seq in research and drug discovery
Attending RNA-Seq 2013 will arm you with the knowledge and skills you need to optimize the practical application of RNA-Seq technology in your lab.
Whether you’ve been using RNA-Seq for years and feel relatively well established, or it’s a totally new addition to your research programs, this agenda has been designed for you.
- Hear pioneering case studies on the most innovative applications of RNA-Seq so that you can return to the lab and put into operation immediately
- Discover how to cost-effectively manage the transition from microarray to RNA-Seq and ensure the hassle-free integration of technologies and data sets
- Leverage the latest advances in RNA-Seq technology for drug discovery and development by meeting with you’re the experts from universities, pharma and genome institutes
Incoming search terms:
- deep sequencing illumina course 2013
Social Networking Pages
-
SEQanswers – RNA Sequencing- DESeq; can I omit timepoints during dispersal estimation? May 24, 2013I have a bacterial timecourse with 2 biological replicates per timepoint. There is a fair bit of variance between my replicates. I have spent the... […]amcloon
- HT Seq Count stranded options May 24, 2013I am very new to bioinformatics, so I would be really grateful for some help! I have been using *HTSeq Count v0.5.3* and I am bit confused about... […]qwrissie
- Tophat 2.0.8b installation error May 24, 2013I install tophat-2.0.8b to rerun the mapping. but when i make it, the error appears like this. make[1]: Entering directory... […]canhu
- reason for low mapping rate?? May 23, 2013we did RNASeq using HiSeq 2000 100PE. When the data were back, I mapping them to the reference sequence, but got very low mapping rate (30-40%). I... […]miaom
- cross-species data - questions about normalization May 23, 2013Hi, I have some data form various samples (cell types) in different species. I want to compare and analyze gene expression variability across the... […]trelek2
- CuffDiff strange output May 23, 2013Hi, I hope that someone can be so gentle to help me. I'm analizing some data from RNA-Seq with TopHat and Cufflinks and I focus my attention on... […]Pruexel
- DESeq; can I omit timepoints during dispersal estimation? May 24, 2013
- Biostar – RNA-Seq
- Why am I getting so many unmapped reads in STAR, classified as "too short"?I am currently using STAR to map several Hi-SEQ mRNA runs. I'm having trouble getting a decent amount of reads to map, but I don't really understand why. I'm hoping you can shed some light :) In the final log, only about 50% (or less) of the reads map to the reference. I'm using a GTF in addition to the genome. The unmapped bin that most […]
- What are the best practices for SNP identification in RNA seq transcriptome dataI have 20 RICE RNA seq tranascriptome data hiseq 2000 platform paired end reads. I aligned fasta reads with BWA and remove PCR duplicates with PICARD. Later I call SNP with samtools using various parameters. I would like to clarify what parameters should I used while alinging to reference rice genome for looking SNP location 100 bp upstream and 250 bp downst […]
- How do TopHat options -g , --supress-hits, and Bowtie options interplay?Hi, I am currently using TopHat2 to map RNA-seq runs. I think there have been some changes pertaining the -g option. Does anyone know how it works now? I used to think that setting -g would look for n alignments for a given read, report them [if top-scoring] and discard those reads that had more than g [top scoring] alignments. Now, the description sounds mo […]
- What happened to -k in TopHat for multiple-mapping reads?Selecting -g n in tophat does not discard reads mapping more than n, but instead only reports n alignments for those out all all their TOP scoring alignments. I think there used to be an option -k that would allow one to discard reads that topped x alignments -- whatever happened to that? I only see -g in the tophat 2 manual, no reporting options like before […]
- Does tophat use the library-type information for mapping, or just for the XS flag?When I specify library-type to TopHat, i.e., first-strand, second-strand, unstranded, TopHat appends a value + or - to the XS:A flag, which is useful for subsequent analyses, such as annotation. However, does this information actually influence the "mappability" of reads, or is this unaffected? My thinking is that the information would be considere […]
- Purpose of Y-shaped adapters in Illumina Sequencing?Hi all, Y adapters different sequences to be annealed to the 5' and 3' ends of each molecule in a library. The arms of the Y are unique, and the middle part, connected to the DNA fragment, is complementary. What are the advantages of this? My take of this over having fully-complementary adapters (ADAPTER1 - - - - - ADAPTER1) is that: -Upon primer a […]
- Why am I getting so many unmapped reads in STAR, classified as "too short"?