RNA-Seq Blog

RNA-SEQ NEWS

Single-cell RNA-Seq gives scientists unprecedented view of brain development

Detailed measurements of genes in individual brain cells allows scientists to trace specific developmental trajectories in the cerebellum Researchers at St. Jude Children’s Research Hospital have created a massive database ...

BGP – identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process

6 days ago Leave a comment 469 Views

High-throughput single-cell gene expression experiments can be used to uncover branching dynamics in cell populations undergoing differentiation through pseudotime methods. Researchers from...

iSEE – an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects

6 days ago Leave a comment 1,004 Views

Data exploration is critical to the comprehension of large biological datasets obtained by high-throughput assays such as sequencing. Interactive exploration fosters the generation of novel data-driven hypotheses...

Vex-seq – high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

7 days ago Leave a comment 701 Views

Understanding the functional impact of genomic variants is a major goal of modern genetics and personalized medicine. Although many synonymous and non-coding variants act through altering the...

Medicare covers Veracyte’s RNA-Seq based Envisia Test

7 days ago Leave a comment 353 Views

The Envisia Genomic Classifier test for idiopathic pulmonary fibrosis (IPF) diagnosis received a draft Medicare local coverage determination (LCD) through the MolDx (Molecular Diagnostics) service program...

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Jobs

Postdoc in Bioinformatics

13 days ago Leave a comment 266 Views

Description: A bioinformatics postdoc position is available at the UCSF Benioff Children’s Hospital Oakland Research Institute. Our research group is interested in examining gene expression (from RNA-seq data) at multiple ...
Read More »
Postdoctoral Position, RNA next-generation sequencing R&D

29 days ago Leave a comment 333 Views
Featured RNA-Seq Job – Scientist II, Translational Genome Sciences

August 20, 2018 Leave a comment 604 Views
Post-doc position in single-cell RNA-seq analysis

August 20, 2018 Leave a comment 339 Views
Featured RNA-Seq Job – Genomics and Bioinformatics

August 15, 2018 Leave a comment 714 Views

Industry News

Medicare covers Veracyte’s RNA-Seq based Envisia Test

7 days ago Leave a comment 353 Views

The Envisia Genomic Classifier test for idiopathic pulmonary fibrosis (IPF) diagnosis received a draft Medicare local coverage determination (LCD) through the MolDx (Molecular Diagnostics) service program...
Read More »
Horizon Discovery announces collaboration with major pharmaceutical company on single cell RNAseq-linked CRISPR screening

20 days ago Leave a comment 508 Views
10X Genomics secures partners to develop applications for its new single cell feature barcoding technology

August 1, 2018 Leave a comment 1,189 Views
BD launches simultaneous RNA and protein expression analysis assay

July 27, 2018 Leave a comment 1,426 Views
Takara Bio strengthens its IP position on single cell RNA-seq

July 20, 2018 Leave a comment 829 Views

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 [...]

Bio-On-Magnetic-Beads (BOMB): Open platform for high-throughput nucleic acid extracti

Hi All, I was thinking this might be interesting for some doing RNA/DNA sequencing. We have establis [...]

Splice donor site mutation

Hello I am having a missense mutation at the last base of exon i.e. exon 13 of a gene having 15 codi [...]

Dealing with low read count in some samples

Greeting Members I have an experiment with 4 time points and 5 biological replicates and each biolog [...]

What is ERCC spike-in really saying about my sequencing run?

I've used ERCC spike-in to prep the library for my recent run of sc-RNA seq. Looking at the plo [...]

Stringtie assembler to assemble Rampage data

Hi, I am curious to know if anyone has tried using Stringtie to improve assembly of transcripts esp [...]

No RIN value output in bioanalyzer

Hi I have just run the bioanalyzer for the first time. I was able to obtain a RIN number of 8 for my [...]

Featured Presentations

Bioconductor Workshop: RNA Seq and ChIP Seq Analysis

13 days ago

RNA modifications poster – Discover the chemical structure of different RNA modifications and their distribution and function in mRNA and tRNAs

July 17, 2018

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

March 21, 2018

RNA-Seq Blog Transcriptome Research & Industry News

RNA-SEQ NEWS

Single-cell RNA-Seq gives scientists unprecedented view of brain development

BGP – identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process

iSEE – an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects

Vex-seq – high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

Medicare covers Veracyte’s RNA-Seq based Envisia Test

Jobs

Postdoc in Bioinformatics

Postdoctoral Position, RNA next-generation sequencing R&D

Featured RNA-Seq Job – Scientist II, Translational Genome Sciences

Post-doc position in single-cell RNA-seq analysis

Featured RNA-Seq Job – Genomics and Bioinformatics

Industry News

Medicare covers Veracyte’s RNA-Seq based Envisia Test

Horizon Discovery announces collaboration with major pharmaceutical company on single cell RNAseq-linked CRISPR screening

10X Genomics secures partners to develop applications for its new single cell feature barcoding technology

BD launches simultaneous RNA and protein expression analysis assay

Takara Bio strengthens its IP position on single cell RNA-seq

Featured Presentations

Bioconductor Workshop: RNA Seq and ChIP Seq Analysis

RNA modifications poster – Discover the chemical structure of different RNA modifications and their distribution and function in mRNA and tRNAs

Mastering RNA-Seq Data Analysis – A critical approach to transcriptomic data analysis

Single cell RNA sequencing and multiple myeloma

MaRS: 27,000 human RNA-Seq in one database

Single-Cell RNA-Seq and cell heterogeneity in the central nervous system

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

Single cell RNA sequencing and Multiple Myeloma

Transcriptome Analysis using RNA-Seq Data

The Iso-Seq method for transcriptome analysis and genome annotation

Single cell RNA-sequencing in idiopathic pulmonary fibrosis

Introduction to RNA-Seq for Researchers

GraphDDP – a graph-embedding approach to detect differentiation pathways in single-cell-data using prior class knowledge

Single-cell RNA-Seq gives scientists unprecedented view of brain development

BGP – identifying gene-specific branching dynamics from single-cell data with a branching Gaussian process

iSEE – an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects

Vex-seq – high-throughput identification of the impact of genetic variation on pre-mRNA splicing efficiency

Medicare covers Veracyte’s RNA-Seq based Envisia Test

Upcoming Webinar – ChIP-Seq / ATAC-Seq Analysis and Integration with Gene Expression Data

Ambiguous splice sites distinguish circRNA and linear splicing in the human genome