RNA-Seq Blog

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Transcriptome and targetome analysis in MIR155 expressing cells using RNA-seq

June 30, 2010 Leave a comment 1,920 Views

Previous studies have demonstrated the utility of microarray expression analysis to identify potential microRNA targets. Nevertheless, technical limitations intrinsic to this platform constrain its ability to fully exploit the potential ...

Ensembl Update (e58) with RNA-Seq Data

June 25, 2010 Leave a comment 2,013 Views

Zebrafish RNASeq models (Zebrafish) A new set of gene models made using RNA-Seq data from 9 tissues. The gene set has exon and transcript level RPKM values for each tissue ...

DESeq – Digital gene expresion analysis based on the negative binomial distribution

June 25, 2010 Leave a comment 2,550 Views

Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal in these data needs to take ...

MapPER – A New Tool for Aligning Paired-end RNA-seq Data

June 24, 2010 Leave a comment 1,944 Views

A Probabilistic Framework for Aligning Paired-end RNA-seq Data Motivation: The RNA-seq paired-end read (PER) protocol samples transcript fragments longer than the sequencing capability of today’s technology by sequencing just the ...

Featured Review Articles – Transcriptomics

June 23, 2010 Leave a comment 4,085 Views

Transcriptomics: Throwing light on dark matter Louisa Flintoft Nature Reviews Genetics 11, 455-455 (July 2010) Transcriptomics: Common disease pathogenesis pathways Gemma K. Alderton Nature Reviews Genetics 11, 386-386 (June 2010) ...

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Featured RNA-SEQ Events

RNA-Seq Summit 2018

January 12, 2018

Single Cell RNA Sequencing – Workshop

December 22, 2017

London Calling 2018

October 22, 2017

RNA 2018 Conference

September 6, 2017

Jobs

Featured RNA-Seq Job – Bioinformatics/Scientist RNA Biology (NCI)

10 days ago Leave a comment 766 Views

We are looking for a Bioinformatics/Scientist to provide dedicated bioinformatic support to the newly formed RNA Biology Laboratory in the Center for Cancer Research, National Cancer Institute. The RNA Biology Laboratory carries out cutting-edge...
Read More »
Featured RNA-Seq Job – Bioinformatics Scientist

17 days ago Leave a comment 1,065 Views
Postdoctoral fellowship in genetic epidemiology

23 days ago Leave a comment 484 Views
Featured RNA-Seq Job – Research Associate

24 days ago Leave a comment 562 Views
Open position for a biostatistician / computational biologist

March 26, 2018 Leave a comment 1,535 Views

Industry News

Biostars RNA-Seq
SEQanswers - RNA Sequencing

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 [...]

Public Rnaseq/Dnaseq Data

Hi, I understand this might be a long shot, but : is anybody aware of a public dataset which contain [...]

error in STAR

Hello, When I ran STAR, it happens like this: Anyone has suggestion? Thanks in advance for great hel [...]

DEXseq in a docker environment

I am attempting to run a DEXseq python script to count reads from a STAR alignment to the human geno [...]

Advice for scRNA-seq Data

Hi, I am new to both scRNA-seq and this forum so hopefully this is posted in the correct place. I ha [...]

FeatureCounts high counts with strand 0,1,2 option

Dear featureCounts developers, I am working on RNASeq data which is generated using Truseq straded H [...]

Inconsistent RNAseq data in knockdown expt

Hi, I am helping a colleague to conduct a differential expression analysis with RNAseq data but I ha [...]

low GC% peak in one end of paired end reads

Hi, I have paired end RNA seq data prepared from Brassica napus using TruSeq kit. After adapter trim [...]

Evaluation of two main RNA-seq approaches for gene quantification in clinical RNA sequencing: polyA+ selection versus rRNA depletion

March 21, 2018