• Subscribe to the RNA-Seq Blog

  
  

  
  Or subscribe by RSS Reader
  
• 5,982 feed subscribers
• 
  

• Featured Events

  

• 

• 

• Media Partners

  
  

• 

• Polls

  How long have you been involved with RNA Sequencing?

  • Just now learning about RNA-Seq
  • less 1 year
  • more than 1 year
  • more than 2 years
  • more than 3 years
  • more than 4 years
  • more than 5 years

  View Results

   Loading ...
• Search for:

• Data Analysis Tools

  Transcriptome Assembly Tools

  Expression & Quantification

  Unpliced Mapping Tools

  Splicing and Junction Mapping

  Analysis Pipelines

  Clouding Platforms

  Databases

  Other Tools

• Tag Cloud

  allele-specific expression alternative splicing bioconductor bioinformatics breast cancer broad institute chip-seq cloud computing cufflinks Data Analysis data analysis pipeline deep sequencing de novo assembly differential expression encode ensembl expression analysis galaxy gene expression high-throughput sequencing illumina ion torrent junction mapping library preparation life technologies lncrna microarray microarrays microrna mirna next-generation sequencing next-gen sequencing pacific biosciences poll results RNA-Seq rnaseq rna sequencing roche tophat transcriptome transcriptome analysis transcriptome assembly transcriptomes transcriptome sequencing transcriptomics

  WP Cumulus Flash tag cloud by Roy Tanck requires Flash Player 9 or better.

• Categories

  Select Category Advertisers Analysis Pipelines Annotation Clouding Platforms Controls Data Analysis Data Analysis Data Sets Databases Events Expression and Quantification Grants / Funding Industry News Information Jobs Library Preparation Methods News Other Tools Patents Pathway Analysis Poll Results Presentations Press Release Publications Reader Conributions Request for RNA-Seq Services Review Sequencing Protocols SNP Detection Splicing and Junction Mapping Statistical Analysis Transcriptome Assembly Tools Transcriptome Sequenced Uncategorized Unspliced Mapping Tools Web Tools Workflow
• 
  
  

• Recent Comments

  • Brian Haas on Interview – Brian Haas Manager of Genome Annotation, Outreach, Bioinformatics and Analysis Broad Institute
  • Bret on The Magic of RNA-Seq
  • Bob Copeman on RobiNA – a user-friendly, integrated software solution for RNA-Seq-based transcriptomics
  • Oz Solomon on Expression Analysis Announces 2013 Grant Program
  • Dr. Jayakishan Meher on Bioinformatics postdoctoral research fellowship available

• Popular Search Terms

  • grape
  • tirthadipa pradhan
  • rna seq analysis
  • rna-seq analysis
  • next generation sequencing ppt
  • rna seq data analysis
  • rna seq vs microarray
  • wine grapes
  • RSEM
  • mangrove

• Recent Search Terms

  • pjlnjcvlt
  • zggwcnpdyzw
  • multiplex rna-seq analysis
  • rna-seq multiplex
  • ion torrent mirna seq analysis
  • transcriptome
  • comparison edger deseq
  • rna-seq 75 or 100 bp
  • rna sequencing reads per library
  • rna seq data analysis

• Archives

  • May 2013
  • April 2013
  • March 2013
  • February 2013
  • January 2013
  • December 2012
  • November 2012
  • October 2012
  • September 2012
  • August 2012
  • July 2012
  • June 2012
  • May 2012
  • April 2012
  • March 2012
  • February 2012
  • January 2012
  • December 2011
  • November 2011
  • October 2011
  • September 2011
  • August 2011
  • July 2011
  • June 2011
  • May 2011
  • April 2011
  • March 2011
  • February 2011
  • January 2011
  • December 2010
  • November 2010
  • October 2010
  • September 2010
  • August 2010
  • July 2010
  • June 2010
  • May 2010
  • April 2010
  • February 2010
  • January 2010
  • January 2009

from Wikipedia, the free encyclopedia

• 1 Introduction
• 2 List of bioinformatics tools associated with RNA-Seq
  • 2.1 Quality control and filtering data
  • 2.2 Short (Unspliced) aligners (see also HTS Mappers)
  • 2.3 Spliced aligners
  • 2.4 Quantitative analysis
  • 2.5 Differential expression
  • 2.6 Statistical analysis
  • 2.7 RNA-Seq simulators
  • 2.8 Trancriptome assemblers (Genome-Guided)
  • 2.9 Trancriptome assemblers (Genome-Independent)
  • 2.10 Visualization tools
  • 2.11 Workbench (analysis pipeline)
• 3 References

(read more…)

Incoming search terms:

• rna-seq gene regulatory network
• RNA-seq plant stress experimental design
• bioinformatics rna seq
• bioinformatics tools rna-seq
• rna-seq gene regulatory network clustering
• chip-seq course
• bioinformatics blog list
• rna-seq classes usa
• rna seq blog list tools
• List of RNA-Seq bioinformatics tools

A common question arises at the beginning of every experiment where RNA-Seq is used to detect differential gene expression between two conditions: How many reads should we sequence?

Now, researchers at Boston College have developed Scotty, an interactive web-based application that assists biologists to design an experiment with an appropriate sample size and read depth to satisfy the user-defined experimental objectives. This design can be based on data available from either pilot samples or publicly available datasets.

AVAILABILITY: Scotty can be freely accessed on the web at http://euler.bc.edu/marthlab/scotty/scotty.php

• Busby MA, Stewart C, Miller C, Grzeda K, Marth G. (2012) Scotty: A Web Tool For Designing RNA-Seq Experiments to Measure Differential Gene Expression. Bioinformatics [Epub ahead of print]. [abstract]

Incoming search terms:

• scotty rna-seq
• scotty rnaseq
• scotty: a web tool for designing rna-seq experiments to measure differential gene expression
• scotty rna seq
• scotty software rnaseq

from yjhua2110 at seqanswers.com

We have constructed expression profiles of long noncoding RNAs (lncRNAs, lincRNAs) and protein-coding genes (mRNAs) from RNA-Seq data across 22 normal tissues (Human BodyMap 2.0 data from Illumina) generated by Cabili et al. (Cabili et al. 2011, Genes Dev., 25, 1915-1927.). We hope it will help your research.

(1) User can find tissue-specific lncRNAs and mRNAs and expression pattern of each gene by viewing heatmap constructed by us. (2)Move mouse cursor on heatmap to see details or click lncRNA or mRNA name to launch detail page. (3) Click the title of the heatmap (e.g. gene symbol, lncRNA name, nearest gene, gene symbol, tissues(e.g. liver, lung…)), to sort whole heatmap.

Examples:
(a) access lncRNA expression profiles.

(b) access protein-coding expression profiles:

Incoming search terms:

• integrated analysis of lncrna and mrna
• RNA-Seq: Novel mRNA analysis
• lncrna cancer rna seq
• lncRNA mRNA
• lncrna rna seq cancer
• lncrna and mrna network analysis
• protocal for rna-seq lncRNA
• rna seq lncrna cancer
• rna-seq lncrna analysis
• lncRNAs mRNAs RNAseq

RNA-Seq Atlas is a web-based repository of RNA-Seq gene expression profiles and query tools. The website offers open and easy access to RNA-Seq gene expression profiles and tools to both compare tissues and find genes with specific expression patterns. To enlarge the scope of the RNA-Seq Atlas, the data were linked to common functional and genetic databases, in particular offering information on the respective gene, signaling pathway analysis and evaluation of biological functions by means of gene ontologies. Additionally, data were linked to several microarray gene profiles, including BioGPS normal tissue profiles and NCI60 cancer cellline expression data. The data search interface allows an integrative detailed comparison between the RNA-Seq data and the microarray information.

This database’s large scale RNA-Seq applications are versatile, and will be beneficial in identifying tissue specific genes and expression profiles, comparison of gene expression profiles among diverse tissues, but also systems biology approaches linking tissue function to gene expression changes.

Availability: http://medicalgenomics.org/rna_seq_atlas

Contact: kruppm@uni-mainz.de, teufel@uni-mainz.de

Krupp M, Marquardt JU, Sahin U, Galle PR, Castle J, Teufel A. (2012) RNA-Seq Atlas – A reference database for gene expression profiling in normal tissue by next generation sequencing. Bioinformatics [Epub ahead of print]. [abstract]

Incoming search terms:

• RNA-Seq Atlas
• rna seq atlas
• rna-seq microarray comparison
• rnaseq atlas
• rna-seq data repository
• rna-seq gene expression
• rna seq repository
• rna seq data repository
• rna-seq repository
• RNAseq different expression web tools

Sticking with the theme of plant RNA analysis, (can’t help it, we’re attending the Plant and Animal Genomes Conference this week and have plants on the brain) here is a great set of tools developed by the The Zhao Bioinformatics Laboratory at the Noble Foundation. Some of the goals of this project are:

• to develop graphical models to model and simulate plant transcriptional regulatory networks;
• to develop novel computational algorithms to infer large-scale gene regulatory networks (GRNs) from high throughput functional genomics data in model plants;

Read more

Incoming search terms:

• how to use plant small rna target analysis server
• plant small rna target analysis
• plant transcriptonal regulatoinry netowrk
• rna seq count regulatory network

ReCount is an online resource consisting of RNA-seq gene count datasets built using the raw data from 18 different studies. The raw sequencing data (.fastq files) were processed with Myrna to obtain tables of counts for each gene. For ease of statistical analysis, we combined each count table with sample phenotype data to form an R object of class ExpressionSet. The count tables, ExpressionSets, and phenotype tables are ready to use and freely available here. By taking care of several preprocessing steps and combining many datasets into one easily-accessible website, we make finding and analyzing RNA-seq data considerably more straightforward.

ReCount is available at: http://bowtie-bio.sourceforge.net/recount/

Incoming search terms:

• comparison of tophat cufflink myrna gene-counter
• recount database transcriptome
• recount ngs
• ReCount RNA-Seq

MediSapiens Ltd, has released the most comprehensive map of human gene expression yet for public use. The data is available through a graphical tool, Transcriptome Viewer, allowing exploration of the expression activity of genes across chromosomes in tens of healthy human tissues.

Data upon which this tool is built (over 300 million manually curated data points) were collected from public science and in itself it is the largest fully integrated gene expression collection in the world.

The fully integrated gene expression information is available online at: http://www.medisapiens.com/transcriptome-viewer-overview/

(Read the press release… )

Incoming search terms:

• rna seq animation
• transcriptome viewer
• rna-seq animation
• high throughput rna sequencing animation
• image of cell microtubules
• rna sequencing at harvard
• rna sequencing harvard
• how to make a 3D model of mitochondria
• rna-seq animnation
• rnaseq animation

wapRNA  is a comprehensive web application tool for processing mRNA-seq and miRNA-seq data. This web tool includes four different modules: mRNA-seq and miRNA-seq sequenced from SOLiD or Solexa platform and all the modules were tested on previously published experimental data. It accepts raw sequence data with an optional reads filter, followed by mapping and gene annotation or miRNA prediction. wapRNA also integrates downstream functional analyses such as Gene Ontology, KEGG pathway, miRNA targets prediction and comparison of gene’s or miRNA’s different expression in different samples. Executable packages for installation on user’s local server are provided.

wapRNA is freely available for use at: http://waprna.big.ac.cn

• Zhao W, Liu W, Tian D, Tang B, Wang Y, Yu C, Li R, Ling Y, Wu J, Song S, Hu S.(2011) wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics [Epub ahead of print]. [abstract]

Incoming search terms:

• Illumina and Solexa
• waprna a web based application for the processing of rna sequences

contributed by an RNA-Seq blog reader…

There is a new genome browser for Culex, Anopheles and Aedes aegypti located at http://aedes.caltech.edu.   In the aedes aegypti genome browser there is a 50-RNA seq sample developmental timecourse (both small-RNAs and poly A track). The paper is out for review.

Incoming search terms:

• anopheles
• aedes aegypti ribosomal rna gff file
• mosquito genome
• essay mosquito genome
• anophles and aedes
• culex mosquito
• anopheles pdf
• info aedes org pe
• insect RNA-SEQ
• aedes aegypti rna-seq

FlyBase has just incorporated several new RNA-Seq data sets from the modENCODE project. These data sets differ from our current RNA-Seq data in that the expression is displayed by strand. One of these data sets includes temporal expression data from the embryonic stages. The other data sets include expression data from a selection of tissues and timepoints, and under a variety of treatments. RNA-Seq expression data, by strand, from cell lines (e.g. Kc, S2) is also now available.

The Treatment Data represents the transcriptome of 4-day old mated adult flies and/or feeding third instar larvae that were fed or exposed to various toxins or environmental stress factors encountered in nature. The concentrations and exposure times used in this study were taken from previously published experiments or were based on experimentally determined LD50 results when there were no preexisting data available. These data can be viewed on GBrowse by selecting the Data Source menu option “D. melanogaster RNA-Seq Data” and selecting the appropriate tracks.

(read more… )

Incoming search terms:

• RNA seq in Drosophila
• RNA-Seq gbrowse log

• 

• 

• 

• 

• Social Networking Pages

  

• 

• SEQanswers – RNA Sequencing

  • standard of clean data May 21, 2013
    Hi all I recently got my prokaryotes RNA-seq data report back. the standard filter steps of the raw data set by our local sequencing center is as... […]
    Pengfei Liu
  • Problem with cummeRbund diffData() May 20, 2013
    Hi all, I'm running Tophat/cufflinks/cuffdiff for differential gene expression and analysis with cummeRbund (v 2.0.0). I'm having an issue with... […]
    Enrique Zudaire
  • How to increase rowsize in heatmap? May 16, 2013
    Hi, I am a complete newbie to all things cummeRbund and am currently fighting with generating readable heatmaps. When I use ... […]
    Mags
  • novoalign mapping May 15, 2013
    Hi, I want to use novoalign to map reads - allowing up to 15 mismatches for 100 bp paired-end reads I am new to novoalign(went through the... […]
    abh
  • Design of expt across multiple lanes May 15, 2013
    Hi, I am performing an RNA-seq experiment to look at differential expression. The design is as follows: 2 populations x 3 biological... […]
    jbono
  • RNA kinds expected in RNA-seq results May 15, 2013
    Hi, We use RNA isolation and library preparation protocols which capture polyadenylated RNA. My question is what kinds of RNA can we expect to... […]
    Kocur

• Biostar – RNA-Seq

  • 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 tag, which is useful for subsequent analyses, such as annotation. However, does this information influence the "mappability" of reads, or is this unaffected? My guess is that the information will be considered for mapping […]
  • 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 […]
  • Cell Type composition in a tissue based on gene marker expression
    I am not sure if the following would even make sense.... Tissues are composed of composite cell types, and often there are studies such as microarray/NGS where we perform a collective sampling of cells from these tissues. Information about the composition (say percentage of cell type) is not taken into consideration. In some case (such as brain/cancer), ther […]
  • Which SNP caller / method to use after aligning RNA-seq with TopHat
    Which SNP caller / method can / should I use after aligning RNA-seq data with TopHat? For genomic data I use GATK, but supposedly it is not just as easy as running GATK on the TopHat RNA-seq data. The team from Broad has no information / documentation on how to use GATK for RNA-seq data. I don't have any variants yet from DNA re-sequencing. […]