RNA-Seq Blog

RNA-SEQ NEWS

Scientists using RNA-Seq close in on origins of chronic pain

T System Collaboration Studies Human Nerve Cells for Genes Tied to Neuropathy A new study by researchers at The University of Texas at Dallas, UT MD Anderson Cancer Center, UT ...

Network meta-analysis correlates with analysis of merged independent transcriptome expression data

7 days ago Leave a comment 591 Views

Using meta-analysis, high-dimensional transcriptome expression data from public repositories can be merged to make group comparisons that have not been considered in the original studies. Merging of...

Single cell combinatorial indexing reveals a landscape of mammalian development

7 days ago Leave a comment 1,160 Views

New technology enables single cell analysis of mouse embryonic development Scientists from Seattle and Berlin have published an atlas on mouse embryonic...

Wanted – RNA-seq bioinformatics wizard with interest in curing cancer

8 days ago Leave a comment 538 Views

Location: Beverly, MA Department: Boston Lab Type: Full Time Min. Experience: ExperiencedCompany DNA: Genomic Expression is finding the best drug for the patient and the best patient for the drug ...

Extracting allelic read counts for variant detection from the Sequence Read Archive

11 days ago Leave a comment 667 Views

The Sequence Read Archive (SRA) contains over one million publicly available sequencing runs from various studies using a variety of sequencing library strategies. These data inherently contain information about underlying genomic sequence variants which...

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Jobs

Wanted – RNA-seq bioinformatics wizard with interest in curing cancer

8 days ago Leave a comment 538 Views

Location: Beverly, MA Department: Boston Lab Type: Full Time Min. Experience: ExperiencedCompany DNA: Genomic Expression is finding the best drug for the patient and the best patient for the drug ...
Read More »
Postdoc Position Available – Computational Genomics

15 days ago Leave a comment 696 Views
Featured RNA-Seq Job – Research Associate Platform Discovery: Single-Cell RNA-Seq

21 days ago Leave a comment 475 Views
Computational Scientist / Data Manager Position Open – Mount Sinai, New York

21 days ago Leave a comment 969 Views
Computational Scientist Position Open – Human Cell Types at Allen Institute

January 22, 2019 Leave a comment 743 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 [...]

DESeq2: model design in rna seq - person variability

I have 8 samples that correspond to 4 persons measured in two times, 0h and 20h. names_chip person t [...]

Denovo assembly system resources

Hi, Hope someone can help me out with an IT/Systems question. I currently process fastq files using [...]

Optimal RNA prep from whole mouse tissue

I have an experiment planned in which RNA samples will be collected from total mouse tissue (eg whol [...]

Optimal RNA preservation pre-sample prep over long time

I have an experiment planned in which RNA samples will be collected during a clinical study over the [...]

Need help about depth difference of biological replicate

Hi, I am very novice about statistics and data analysis. Recently we have done some RNA sequencing w [...]

error in DESeqDataSet

Dear all, I have 4 RNAseq file from an experiment with two different conditions, "Untreated [...]

RNAseq from patients

Hello, I have a question, If I have 10 Bam files (RNAseq) from 10 different patients and I want to s [...]

visualizing RNAseq mapping to reference

I'm using Geneious (for Windows), which has two RNA Seq mappers (Geneious RNA Mapper, and BBmap [...]

ERCC spike-ins for prokaryotes

Hi! I see that many people use ERCC spike-ins with prokaryotes, but looking at the manufacturer desc [...]

RNAseq without technical replicates

Dear all, I want to download RNAseq files of tumor cell lines from GEO and compare between them. I k [...]

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

Scientists using RNA-Seq close in on origins of chronic pain

Network meta-analysis correlates with analysis of merged independent transcriptome expression data

Single cell combinatorial indexing reveals a landscape of mammalian development

Wanted – RNA-seq bioinformatics wizard with interest in curing cancer

Extracting allelic read counts for variant detection from the Sequence Read Archive

Jobs

Wanted – RNA-seq bioinformatics wizard with interest in curing cancer

Postdoc Position Available – Computational Genomics

Featured RNA-Seq Job – Research Associate Platform Discovery: Single-Cell RNA-Seq

Computational Scientist / Data Manager Position Open – Mount Sinai, New York

Computational Scientist Position Open – Human Cell Types at Allen Institute

Industry News

sRNAlytics receives FDA support for an AI-powered, small RNA sequencing analysis platform

Canopy Biosciences exclusively licenses technology for error correction in NGS from Washington University

RNA Sequencing identifies new cannabis pathogen

Oxford Nanopore introduces new cDNA kits for transcriptome sequencing

Fluidigm introduces REAP-Seq for multi-omic single-cell analysis on the C1

Featured Presentations

Integrative Genomics Viewer – RNA-Seq Data Basics

Genetic analysis of differentiating cells using single-cell RNA-seq

RNA Sequencing – Case Studies & Clinical Relevance

MSI Tutorial – RNA Sequencing Analysis

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

Sparse full length sequencing – a highly multiplexed ribosomal RNA depletion-based RNA sequencing platform

Upcoming – Microsymposium on Small RNA Biology

Cell Population Mapping – cell composition analysis of bulk genomics using single-cell data

sRNAlytics receives FDA support for an AI-powered, small RNA sequencing analysis platform

The impact of heterogeneity on single-cell sequencing

Scientists using RNA-Seq close in on origins of chronic pain

Network meta-analysis correlates with analysis of merged independent transcriptome expression data

Single cell combinatorial indexing reveals a landscape of mammalian development