RNA-Seq Blog

RNA-SEQ NEWS

New deep learning tool gives RNA sequencing data some context

July 24, 2018 Leave a comment 1,732 Views

Researchers at Oregon State University have used deep learning to decipher which ribonucleic acids have the potential to encode proteins. The gated recurrent neural network developed in the College...

netSmooth – network-smoothing based imputation for single cell RNA-seq

July 23, 2018 Leave a comment 1,471 Views

Single cell RNA-seq (scRNA-seq) experiments suffer from a range of characteristic technical biases, such as dropouts (zero or near zero counts) and high...

Post-doc position available – RNA-Seq

July 23, 2018 Leave a comment 809 Views

Generate transcriptomics data resulting from Prostate Cancer patients exosomes to detect biomarkers indicative of aggressive prostate cancer. This includes handling patient tissue, urine and...

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

July 20, 2018 Leave a comment 1,326 Views

Retinal ganglion cells (RGCs) convey the major output of information collected from the eye to the brain. Thirty subtypes of RGCs have been identified...

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

July 20, 2018 Leave a comment 989 Views

Takara Bio USA, Inc has announce that patent JP6336080B—covering the Smart-seq2 method, developed by Rickard Sandberg and exclusively licensed to TBUSA by the Ludwig Institute—has...

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Jobs

Postdoc Position: Bioinformatics of Long Noncoding RNA Functional Elements

6 days ago Leave a comment 290 Views

The “Genomics of Long Non-Coding RNAs in Disease” Laboratory (GOLD Lab) at the University of Bern has an opportunity for a Bioinformatics Postdoc. The Project: Understanding how long noncoding RNA ...
Read More »
Featured RNA-Seq Job – Research Assistant

October 1, 2018 Leave a comment 648 Views
Bioinformatician and Data Engineer

October 1, 2018 Leave a comment 680 Views
Postdoc in Bioinformatics

September 6, 2018 Leave a comment 714 Views
Postdoctoral Position, RNA next-generation sequencing R&D

August 21, 2018 Leave a comment 741 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 [...]

RNA-seq data on single nucleotide level (time series data)

Hello, I want to work with multidimensional RNA-Seq dataset on single nucleotide level. anyone have [...]

Failure of tumor FFPE samples sequencing

Dear all, I am a PhD student in Belgium, Brussels, working on RNA sequencing of ~130 tumoral FFPE sa [...]

Trinity Adapter Trimming: Clontech and Illumina?

Apologies for what is an often repeated topic, but with (I believe) a new twist. I have several RNA [...]

miRNA/smallRNA adapter triming: recommendations for adaptor error rate and Q-trim

I am looking for recommendations on how to trim miRNA/smallRNA sequencing data because the trimming [...]

scRNA-seq

Dear all, registration is now open for our course "Analysis of single cell RNA-seq data" i [...]

DGE analysis with >3 treatements

Hello, I have 2 different phenotypes sampled in three populations, with three reps each. I performed [...]

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

New deep learning tool gives RNA sequencing data some context

netSmooth – network-smoothing based imputation for single cell RNA-seq

Post-doc position available – RNA-Seq

Single cell transcriptome profiling of retinal ganglion cells identifies cellular subtypes

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

Jobs

Postdoc Position: Bioinformatics of Long Noncoding RNA Functional Elements

Featured RNA-Seq Job – Research Assistant

Bioinformatician and Data Engineer

Postdoc in Bioinformatics

Postdoctoral Position, RNA next-generation sequencing R&D

Industry News

1CellBio and the Open Medicine Institute to Demonstrate Power of Single-Cell RNA Sequencing in Precision Medicine Applications

Advaita Bioinformatics has announced a new release of their advanced RNA-seq and gene expression analysis software, iPathwayGuide

Illumina to acquire Pacific Biosciences for approximately $1.2 billion

Machine learning analysis of RNA-Seq data to de-risk repositioning of existing FDA-approved drugs

Proteona licenses ESCAPE RNA Sequencing Technology from NUS

Featured Presentations

Differential Splicing Analysis with RNA-Seq: Current Applications, Approaches, & Limitations

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

Upcoming symposium – Genomics based biomarker discovery in cancer

Portcullis – efficient and accurate detection of splice junctions from RNA-Seq

1CellBio and the Open Medicine Institute to Demonstrate Power of Single-Cell RNA Sequencing in Precision Medicine Applications

Comprehensive evaluation of RNA-Seq analysis pipelines in diploid and polyploid species

RNA-Seq reveals new clues to the origin and progression of multiple sclerosis

Single-cell RNA-Seq identifies cell-cell communication associated with tumor characteristics

Single-cell analysis reveals how melanoma cells resist immunotherapy

DASHR 2.0: Integrated database of human small non-coding RNA genes and mature products