• Subscribe to the RNA-Seq Blog

  
  

  
  Or subscribe by RSS Reader
  
• 6,119 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 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 small rna 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

  • deseq vs rpkm
  • Zea mays
  • rna sequencing tag multiple samples
  • rna-seq workshops
  • tophat2 mapping quality
  • gene expression in different tissues rna seq
  • lifescope mapreads parameters
  • rna seq vs microarray
  • RNA-Seq Library Preparation
  • rna seq data analysis step by step

• 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

Measures aim to ensure sustained success in a fast-changing market environment

Roche today announced changes to the management and set-up of its life-science business. The Applied Science Business Area will be dissolved and its portfolio of products integrated within Roche’s other Diagnostics Business Areas.

Following assessment of its sequencing R&D portfolio, Roche has decided to:

1. Return the ISFET project for the development of a semiconductor-based sequencing system to DNA Electronics. The project was a partnership with 454 Life Sciences.  Roche believes that it will be unable to disrupt the market with the product at launch.
2. End its partnership with IBM for the development of a nanopore-based sequencing platform due to high technical risks involved.
3. Establish a dedicated unit to focus solely on sequencing. This unit will be tasked with implementing a sequencing strategy from life-science research to clinical diagnostics, explore internal and external opportunities that can provide customers with differentiated products, and will also manage Roche’s existing sequencing business.

The price pressure and funding cuts in life-science research that have been features of the market environment for some time now are expected to continue. The organisational arrangements Roche is introducing are designed to further improve productivity and enhance the market responsiveness of its life-science business, which currently accounts for about 7 % of total Diagnostics sales.

As a consequence, the Applied Science business area will be dissolved as of the end of 2013.

Changes expected to affect approximately 110 positions in Penzberg (Germany) and 60 positions in Branford (Connecticut, USA), the home of its 454 Life Sciences business.

(read the entire press release…)

Incoming search terms:

• targeting drug rna-sequencing
• www rna-seqblog com roche-to-reorganize-sequencing-business
• roche 454 ibm
• introduction to fragment whole transcriptome rna blog
• sequencing business market share
• SwitchGear Genomics Inc
• roche sequencing business
• roche reorganization 2013
• roche cut 454
• roche and sequencing business

First high-throughput sequencing platform to deliver one million reads with read lengths of up to 1000 bp and beyond.

Roche announced today the launch and immediate availability of a new software package (v2.8) that significantly improves long-read shotgun sequencing performance on its GS FLX+ System. This system is the first high-throughput sequencing platform to deliver one million reads with accuracy and length that are comparable to traditional Sanger-based methods. The improvements will allow researchers to discover more novel complex genetic variants and uncover the hidden biology in difficult-to-sequence regions of genomes, transcriptomes, and metagenomic samples. The GS FLX+ System and software will be presented today at the American Society for Human Genetics Annual Meeting in San Francisco. Read more

Incoming search terms:

• rna seq roche
• 454 flxplus amplicon
• junior rna seq
• rna seq roshe
• rna-seq for virology
• RNA-SEQ ROCHE
• RPKM 454 platform
• rpkm 454 sequences
• total rna sequencing roche

Roche is increasing its offer to purchase Illumina from $44.50 to $51 per share. This represents a deal valued at almost $6.6 billion, cash.  Amazing!

Though no deal has yet been struck, because this is a cash deal that has been made public by Roche, the FTC is already investigating the acquisition for violations of antitrust laws.

Illumina has advised their stockholders to defer taking any action in response to Roche’s increased offer.  (Illumina press release)

“Based on our discussions with Illumina shareholders we have seen interest to accelerate the takeover process,” says Severin Schwan, CEO of Roche. “As a result, we are increasing our offer price to $51.00 per share. Roche’s preference continues to be a negotiated transaction. We look forward to the possibility of a swift completion that offers immediate value to Illumina’s shareholders.” (Roche’s press release)

Below is the text of the letter Roche sent on March 29, 2012 to Jay Flatley, President and Chief Executive Officer of Illumina, Inc:

Dear Jay,

Over the past several weeks, we have had a number of productive discussions with Illumina’s shareholders and we have observed the market reaction to our offer to acquire Illumina. We are also cognizant of your statements that you regarded our offer price of $44.50 as insufficient to provide a basis for discussions between our companies.

In light of this, we are increasing our offer for all outstanding shares of Illumina to $51.00 per share. Our revised offer represents a 15% premium to our offer on January 25, 2012 and a substantial premium of 88% over Illumina’s closing stock price on December 21, 2011, the day before market rumors about a potential transaction between Roche and Illumina drove Illumina’s stock price significantly higher. It also represents a 34.1x multiple of Illumina’s projected forward earnings based upon analysts’ current consensus estimates for 2012.

As you know from our prior communications, it has been and remains Roche’s preference to conclude a negotiated transaction with Illumina. We hope that you will agree that our new price presents a very attractive opportunity to your shareholders and that the interests of your shareholders and the fiduciary responsibilities of you and your Board require that you agree to enter into discussions with us.

If you continue to decline to negotiate with us, we will have no choice but to continue our effort to effect a transaction unilaterally. However, I strongly hope that you will either agree to commence discussions with us now or remove all obstacles so that your shareholders can make their own determinations about the adequacy of our increased offer.

I look forward to hearing from you.

Sincerely,

Franz B. Humer
Chairman, Roche Holding Ltd

(read the Genomeweb News story… )

(read the Genetic Engineering News story… )

Incoming search terms:

• RNA seq illumina
• illumina rna seq
• illumina rna sequencing
• illumina roche purchase ppt
• info aedes org pe loc:US

Last week an article appeared in BioArray News as part of the coverage of the ongoing Roche/Illumina story – Illumina Array Customers ‘Apprehensive’ of Possible Roche Takeover, Fear Platform ‘Stagnation’

Yesterday, I received an email from Life Technologies (I guess I’m on their marketing list) that seemed unusual to me.  No message, just an image with a link to the article.

This email was clearly intended to draw attention to the article and highlight the fears of current Illumina customers about the possible deal.  Were they trying to build opposition to the deal?  Do they feel the combined financial strength of Roche and the technical strength of Illumina would be a formidable competitor?  You decide…

Incoming search terms:

• roche life technologies
• life technologies roche
• illumina vs life technologies
• roche to buy life technologies
• roche buy life technologies
• roche life tech
• roche and life technologies
• life technologies vs illumina
• life tech roche
• life technologies takeover

Last week, Roche released a plan to take over Illumina’s Board. Roche announced that it has provided notice to Illumina, Inc. that it will nominate a slate of highly qualified, independent candidates for election to Illumina’s Board of Directors and propose certain other matters for the consideration of Illumina’s shareholders at Illumina’s 2012 annual meeting, which, if adopted, would result in Roche-nominated directors comprising a majority of the Illumina board. Roche also named five alternate nominees for election to Illumina’s board. (see the Roche release…) Read more

On Tuesday, Roche announced a $5.7 Billion hostile takeover bid for Illumina. Roche said it is making its proposal after “multiple efforts to engage with Illumina in order to reach a negotiated transaction,” were rebuffed. Under the terms of its all-cash proposed deal, Roche would acquire all outstanding shares of the San Diego-based next-generation sequencing and microarray firm at $44.50 per share. The bid price is a 61 percent premium over the one-month historical average of Illumina’s share price and 43 percent premium over the firm’s three-month historical average, both as of Dec. 21. (See the Roche Press Release…)

Today,  in response to Roche’s bid for the company, Illumina has created a rights agreement to “deter coercive and otherwise unfair takeover tactics”. The agreement states that if any person or group, such as Roche, becomes the holder of 15 percent or more of Illumina’s stock, then shareholders — excluding those owning 15 percent or more of the stock — would have the right to purchase additional shares at the then-current exercise price (a favorable price), but that the shares would have a market value of twice that exercise price. In other words, the shareholder would be able to buy a share of Illumina at half the market price. (See the Illumina Press Release… )

If completed, the acquisition would combine two of the leading names in next-gen sequencing.

Incoming search terms:

• illumina paired end sequencing video
• --SS_lib_type in trinity for illumina paired end reads

From GenomeWeb

Illumina’s Q3 Revenues Jump 50 Percent on Strength of HiSeq
Illumina reported after the close of the market Tuesday that its third-quarter revenues jumped 50 percent, easily beating analysts’ consensus estimate.

Life Technologies’ Q3 Revenues Rise 8 Percent on Record SOLiD 4 Sales
The company’s CE and next-generation sequencing business saw strong results, while its PCR business suffered from difficult year-ago comparison figures, it said.

Roche’s Sequencing Business Grows 12 Percent YTD as Applied Science Sales Shrink in Q3
Roche said it has seen “robust uptake” in the European Union and Asia Pacific for the 454 GS Junior sequencer, a benchtop sequencer launched in May that is geared at small laboratories.

Helicos BioSciences Cuts 14 More Positions in Q3
The firm also cut 40 jobs in May amid its plans to restructure and focus on the molecular diagnostics market. Part of its restructuring includes the departure of J. William Efcavitch as chief technology officer.

The firm will cut another 14 positions, on top of the previously announced 40 jobs, as it aims to reduce its operating costs. Additionally, Lapidus steps down as Chairman.

Pacific Biosciences Files for IPO in Q3
The firm has raised around $370 million since its inception, and announced plans to go public in an offering that could potentially bring in $200 million.

The firm went on to sell 12.5 million shares at $16 per share, the mid-point of its estimated offering range, at the initial public offering in October.

• 

• 

• 

• 

• Social Networking Pages

  

• 

• SEQanswers – RNA Sequencing

  • HT Seq Count stranded options May 24, 2013
    I 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, 2013
    I 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, 2013
    we 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, 2013
    Hi, 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, 2013
    Hi, 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
  • cannot away with cuffdiff,incredible May 23, 2013
    Hi,all I have 4(A,B,C,D) sample in 4 times(increasing time),I got diff result in 3 different cuffdiff 1.cuffdiff 3(A,B,C) individual... […]
    upper

• 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 data
    I 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 […]