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Microarray analysis workhorse limma – now capable of differential expression and differential splicing analyses of RNA-Seq data

2 days ago 0 749 Views

limma is an R/Bioconductor software package that provides an integrated solution for analysing data from gene expression experiments. It contains rich features for handling complex experimental designs and for information ...

IRcall and IRclassifier – two methods for flexible detection of intron retention events from RNA-Seq data

2 days ago 0 236 Views

The emergence of next-generation RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate detection of intron retention (IR) events from RNA-Seq ...

Complex in vivo RNA-Seq of a Bacterial Pathogen

2 days ago 0 230 Views

Researchers at Umeå University recently found that Yersinia pseudotuberculosis can be used as a model of persistent bacterial infections. They performed in vivo RNA-seq of bacteria in small cecal tissue ...

Partek® Flow® 4.0 Software Brings More Statistical Power, Visualization, and Speed to RNA-Seq Analysis

2 days ago 0 243 Views

ST. LOUIS–(BUSINESS WIRE)-Partek Incorporated announces the newest release of their popular analysis software, Partek Flow 4.0. With new features including multi-factor mixed model ANOVA, Fisher’s exact test, and additional visualizations, ...

Introduction to RNA-Seq Data Analysis

3 days ago 0 579 Views

RNA-seq provide much more information than gene expression microarrays. In additional to gene expressions, it provides informa8on for: alternative splicing – structural changes of genes: Gene fusion. new genes/exons. ...

Exosome isolation and holistic expression profiling using RNA-Seq and RT-qPCR

3 days ago 0 319 Views

Session 3b: Microgenomics and microRNA and NGS Exosome isolation and holistic expression profiling using RNA-Seq and RT-qPCR Michael W. Pfaffl, Technical University of Münich, Germany

Stranded Whole Transcriptome RNA-Seq for All RNA Types

3 days ago 0 314 Views

Stranded whole transcriptome RNA-Seq described in this unit captures quantitative expression data for all types of RNA including, but not limited to, miRNA (microRNA), piRNA (Piwi-interacting RNA), snoRNA (small nucleolar ...

Upcoming RNA-Seq Workshops

23 days ago

NGS Workshop 2015 – A Practical Introduction to NGS Data Analysis

October 29, 2014

Extracellular Biomarkers Summit

October 3, 2014

RNA-Seq Europe 2015

September 17, 2014

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Jobs

Featured RNA-Seq Job – Sr Research Associate- Sequencing Platforms

5 days ago 0 281 Views

Lawrence Berkeley National Laboratory (Berkeley, CA) The Department of Energy (DOE) Joint Genome Institute in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) is searching for an ...
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Featured RNA-Seq Jobs – Project Managers – Transcriptome Analysis

December 23, 2014 0 723 Views
Featured RNA-Seq Jobs – Dec 2014

December 19, 2014 0 692 Views
Google’s Calico begins search for a head of bioinformatics

December 8, 2014 0 929 Views
Featured RNA-Seq Job – Assistant Professor

December 5, 2014 0 737 Views

Industry News

Partek® Flow® 4.0 Software Brings More Statistical Power, Visualization, and Speed to RNA-Seq Analysis

2 days ago 0 243 Views

ST. LOUIS–(BUSINESS WIRE)-Partek Incorporated announces the newest release of their popular analysis software, Partek Flow 4.0. With new features including multi-factor mixed model ANOVA, Fisher’s exact test, and additional visualizations, ...
Read More »
Thermo Fisher Scientific Launches Ion Torrent AmpliSeq RNA Fusion Lung Cancer Research Panel

9 days ago 0 510 Views
Illumina Launches HiSeq X Five System and HiSeq 3000/4000 Sequencing Systems

13 days ago 0 1,044 Views
10X Genomics is commercializing a new genomics platform that will change the definition of sequencing

13 days ago 0 783 Views
Kapa Biosystems Expands Partnership with Roche NimbleGen to Include RNA Sample Preparation for Targeted Next-Gen Sequencing

December 9, 2014 0 591 Views

SEQanswers - RNA Sequencing
Biostars RNA-Seq

P-Val not significant for diff expressed genes

Dear All, I have doubt regarding P-Val of diff expressed genes. kindly help Doubt : I have list of g [...]

HtSeq counts 0 features for mapped reads in sam fliles

Hello, My input : 50 bp RNA Seq single end illumina reads mapped to GRCh 38 from ensemble. Mapping w [...]

RNAseq - Alternatives to SeqScript?

Howdy all, Looking for lower cost alternatives to SeqScript. I realize a big portion of the cost is [...]

What's the best RNA Seq Tuxedo suite tutorial/streamlined intro protocol?

Hi all, new to this community. I've been attempting to learn the Tuxedo suite using their proto [...]

cummeRbund csScatter() error

Hello Can you please help me find out why I am getting this error? Thanks cuff = readCufflinks() [...]

featureCounts 'Found reads that are not properly paired' despite being sorted by STAR

Hi all, I have mapped 101 bp PE reads to GRCh38 and I am using featureCounts for read summarization. [...]

STAR RNA-seq aligner yields different read length than fastqc/zcat?

Hi all, I've noticed that the STAR RNA-seq aligner yields different read length than fastqc/zca [...]

Experimental design for RNA-seq in a non-model plant species

Hi all, I'm newbie of the forum and I have no experience in the RNA-seq technology. My aim is t [...]

MetaR: a simple language useful for RNA-Seq data analysis

Hello, I wanted to introduce MetaR (http://metaR.campagnelab.org), a language to analyze RNA-Seq dat [...]

Quatification of tRNA-derived RNA fragments (tRFs) ?

Hi, In the lab we are analyzing tRNA-derived RNA fragments. My boss needs to quantify these fragment [...]

Newbie question regarding mapping of RNA-seq data

Hi all, I'm stuck with a total newbie problem here. I'm analyzing RNA-seq data from mouse, [...]

High throughput RNA extractions - best methods/kits?

Hi All, We have a large number of RNA samples coming (most likely in Trizol) this year. I'd lik [...]

I got some errors from irap.

I'm trying to analyse my rna-seq data with irap. However, I got some errors during the analysis [...]

De error

Hi, I get the following error when trying to do a DE analysis. /trinityrnaseq_r20140413/Analysis/Dif [...]

Upcoming Workshop: A Beginner's Guide to NGS Data Analysis (early-bird ending today)

*A Beginner's Guide to NGS Data Analysis * *Quality Control, Read Mapping, Visualization and Do [...]

How to correctly estimate RNA-seq mean insert size and standard distribution

Hi SEQanswers community! So I'm not sure if this has been posted - I poked around, but didn [...]

Discovery of protein–lncRNA interactions from large-scale CLIP-Seq and RNA-Seq data

Long non-coding RNAs (lncRNAs) are emerging as important regulatory molecules in developmental, phys [...]

featureCounts: 270 chr in GRCh38 and only assigning 1.5%?

INPUT Stranded RNAseq, 101bp Illumina paired end reads mapped to GRCh38 release 78 using star. COMMA [...]

Parameters to consider for aligning long reads (150bp) in Tophat

Tophat's defaults sets: --read-mismatches 2 --read-gap-length 2 --read-edit-dist 2. This gave m [...]

GalaxyProject-Error Messages

Dear All, I'm currently using GalaxyProject website's RNA sequencing tools to do my RNA se [...]

Rna-Seq Pipeline

So, there're papers on designing an RNA-seq experiment, and normalizing the data (Bullard et. a [...]

Visualisation Of Alternative Splicing Events Using Rna-Seq Data

Hi, I am looking for tools that provide a nice graphical display of different alternative splicing e [...]

How Are Rna-Seq Transcripts Assigned?

I am looking at some RNA-seq data analyzed by cufflinks using standard conditions, and trying to det [...]

Tophat Time And Memory Requirement

Hi, Anyone has an idea of memory and time requirement for tophat 1.4.1 for 76 paired-end reads (~60M [...]

Rna-Seq Data Variant Calling

Has anyone tried calling variants from RNA-seq data and comparing those with WGS/Exome sequencing va [...]

Tutorial: Workshop - Analysis Of Next Generation Sequencing Data

Workshop - Analysis of Next Generation Sequencing Data (Programming for Evolutionary Biology 2012 ht [...]

Searching For A Simple Yet Powerful Workflow For Rna-Seq

Hi, I have to start working with RNA-Seq data and have worked previously with ChIP-Seq so I am famil [...]

Rna-Seq Data For Cd34+ Cells Or An Alternative Approach To Compare My Expression Set

Hi! I am looking for a RNA-seq data on CD34+ cells (human), to compare the expression of genes in my [...]

Distribution Of Isoform Length

Is there any paper that contains the distribution of isoform length in different organisms? Here I [...]

Building A Webpage For Accessing Rna-Seq Expression Data

Hello all, I would like to get some hints to go about this task. I'd like to design a webpage/s [...]

Tophat Error : Oserror: [Errno 2] No Such File Or Directory

Hi, I am running tophat and getting a lot of different errors, I could understand some of them, but [...]

Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]

Hola! I would like to write a quick tutorial on viewing your coverage/track/wiggle files using UCSC. [...]

Why Are There Many Rna-Seq Hits To Intronic Regions?

I am looking at RNA-seq data, which I have little experience in. I notice that for many genes, there [...]

Differential Rnaseq Expression Analysis Directly On Stanford'S Great?

Does anybody know if the tool GREAT from Stanford U. can be used for RNAseq differential expression [...]

De Novo Transcriptome And Comparative Genomics

Hello all, First time posting here. I am looking at doing some comparative genomics with a mammalian [...]

How To Get Equal Numbers Of Gene_Id And Exon_Id For Use In Newexoncountset Function For Dexseq

I'm trying to run DEXseq but am having trouble with the newExonCountSet function because my gen [...]

Is This Always The Case That The Wig/Bigwig/Bed Files Are Meant Only For Viewing Into Ucsc Browser?

Since I'm currently working with RNA-seq experiment data stored in wig/bigwig format. There are [...]

Strand-Specific Rna-Seq Data For Maqc Samples?

Hi, Is there publicly available strand-specific RNA-Seq data for the MAQC samples? It seems that the [...]

Publicly Available Strand-Specific Rna-Seq Data With Corresponding Rt-Pcr Data?

Hi, I'm wondering if there publicly available strand-specific RNA-Seq data with corresponding R [...]

Charateristics Of Strand-Specific Rna-Seq Dataset

Dear all, I would like to ask the difference between strand-specific and not strand-specific dataset [...]