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2^nd Next Generation Sequencing
Boston, MA – May 30^th – 31^st
GTC’s 2nd Next Generation Sequencing Conference is a 2-day meeting that will bring together leading technology and diagnostic companies, national laboratories and academic institutions from across the globe to discuss applications of NGS platforms, novel sequencing strategies, developments in nanopore and single molecule sequencing and the implementation of NGS in the clinical space. (read more…)

Next Generation Sequencing
Prague – June 12^th – 13^th
Informa Life Sciences – Our Next Generation Sequencing conference provides you with the opportunity to hear the latest and most exciting developments in NGS technological advances (including 3rd and 4th generation platforms), sample preparation strategies for difficult samples, and how research, drug/diagnostic discovery and development are utilising next generation sequencing. (read more…)

Next-Gen Sequencing Applications & Translational Technologies Summit
San Francisco, CA – August 6^th – 8^th
ibc Life Sciences – How are others leveraging the power of next-generation sequencing in everyday research, and for clinical and diagnostic applications? Are you looking to accelerate your discovery and development efforts using translational technologies? (read more…)

NGX: Applying Next-Generation Sequencing
Providence, RI – Aug 13^th – 15^th
Cambridge Healthtech Institute’s NGX: Applying Next-Generation Sequencing investigates the expanding applications of NGS. Learn from experienced researchers from large sequencing centers, core laboratories, and specialized groups as they share their practical knowledge, real-world experiences and solutions. (read more…)

Next- Generation Sequencing Summit
London, September 17^th – 18^th
SMi – A data interpretation and analytical perspective. Identifying potential therapeutic drug targets and validating their suitability is a complex process involving numerous experimental platforms, including DNA sequence analysis. (read more…)

Beyond the Genome 2012
Boston, MA – September 27^th 29^th
Genome Medicine and Genome Biology – The aim of the conference is to discuss next-generation sequencing and other new technologies, informatic tools, and how these are being used to identify common and rare disease-causing mutations in the research laboratory and toward the clinic. Themes will include cancer genomics from discovery sequencing to genome guided therapy, epigenomic technologies and applications, and inherited disease beyond the candidate gene approach. There will also be an informatics workshop. (read more…)

Next Generation Sequencing Congress
London – November 15^th-16^th
Oxford Global – 2 day conference showcasing cutting edge next generation sequencing platforms, technologies, applications and computational tools for the analysis of NGS sequencing data. (read more…)

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• SEQanswers – RNA Sequencing

  • 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
  • TopHat extremely low paired mapping rate. PLS HELP! May 22, 2013
    Hey guys, I have some problems with my paried-end RNA seq analysis on Galaxy. As you can see in the bam flagstat output, my tophat alignment rate is... […]
    Felix.Lee
  • Identifying small RNA sequence within whole genome sequence May 21, 2013
    Hi all, I want to know if there are any useful bioinformatic tool to find small RNA sequence within a whole bacteria genome. Thank you in... […]
    Inma
  • 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

• 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 […]