RNA-Seq Blog

RNA-SEQ NEWS

UTAP – user-friendly transcriptome analysis pipeline

RNA-Seq technology is routinely used to characterize the transcriptome, and to detect gene expression differences among cell types, genotypes and conditions. Advances in short-read sequencing instruments such as Illumina Next-Seq ...

RNA sequencing reveals microRNA-like RNAs in fungi

8 hours ago Leave a comment 170 Views

A. oligospora can develop adhesive networks (AN) to capture nematodes. Fungi are the most common cause of diseases in crops and other plants, and pose major threats to humans and other ...

Comparison of RNA-Seq data alignment and qene expression quantification tools for clinical breast cancer research

1 day ago Leave a comment 412 Views

The rapid expansion of transcriptomics and affordability of next-generation sequencing (NGS) technologies generate rocketing amounts of gene expression data across biology and medicine, including...

GSEPD – a Bioconductor package for RNA-seq gene set enrichment and projection display

1 day ago Leave a comment 452 Views

RNA-seq, wherein RNA transcripts expressed in a sample are sequenced and quantified, has become a widely used technique to study disease and development. With RNA-seq, transcription abundance can be measured, differential expression genes...

1CellBio Announces Custom Targeted Bead Program to Accelerate Next Phase in Single-Cell Analysis

1 day ago Leave a comment 281 Views

1CellBio today announced a new program to supply select customers with its proprietary inDrop™ hydrogel beads synthesized with custom primers that target user-specified transcripts. “This new program enables researchers to ...

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Jobs

Seeking Postdoc – Knowledge of de novo genome assembly, transcriptomics analysis (RNA-seq and others), coding in Python, Perl, and/or R

4 days ago Leave a comment 545 Views

Performs bioinformatics analysis, statistical analysis and independently carries out de novo genome assembly, transcriptomic analysis (RNA-seq and other data), and other types of high-throughput sequencing data. Collects, compiles and analyzes data...
Read More »
Featured RNA-Seq Job – Inside Sales / Technical Customer Service

10 days ago Leave a comment 403 Views
Wanted – RNA-seq bioinformatics wizard with interest in curing cancer

March 18, 2019 Leave a comment 749 Views
Postdoc Position Available – Computational Genomics

March 11, 2019 Leave a comment 877 Views
Featured RNA-Seq Job – Research Associate Platform Discovery: Single-Cell RNA-Seq

March 4, 2019 Leave a comment 648 Views

Industry News

Agilent introduces new RNA / DNA QC system for NGS samples

15 days ago Leave a comment 847 Views

Agilent Technologies announced today the shipping of a new instrument that offers laboratories a more low-throughput option for analyzing the quality of RNA and DNA samples. “The Agilent 4150...
Read More »
sRNAlytics receives FDA support for an AI-powered, small RNA sequencing analysis platform

29 days ago Leave a comment 845 Views
Canopy Biosciences exclusively licenses technology for error correction in NGS from Washington University

March 11, 2019 Leave a comment 792 Views
RNA Sequencing identifies new cannabis pathogen

March 8, 2019 Leave a comment 839 Views
Oxford Nanopore introduces new cDNA kits for transcriptome sequencing

February 6, 2019 Leave a comment 1,107 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 [...]

DESeq and checkFullRank(modelMatrix)

Hello guys, I am running DESeq2 to compare 4 different conditions and I have a problem with a commma [...]

HiSAT2 RNAseq alignment low + stranded data predicted to be unstranded

Hi all, I have been receiving some confusing output with an RNA-seq dataset that I am trying to ulti [...]

Control-based correction in multispecies RNAseq comparison

Hi all! I think this issue fits better here than on another forum I posted this question some time a [...]

ligase for ssDNA adapter ligation

Hi, all Could you recommend a ligase for adapter ligation to 3' end of cDNA? or any relevant ar [...]

Counting and Recount reads with featureCotuns

Hello everyone, I am using different tools for getting alignments and read count such as, salmon and [...]

No bam from kallisto or Salmon after piping into samtools

Hi all, I am trying to generate the pseudo bam files from both Kallisto v45 and Salmon v13 and can [...]

StringTie merge- can someone help me understand its output?

Hello, I am currently using StringTie merge on a StringTie output in order to discover genes that ar [...]

STAR Aligner quantMode and fatal error

Hello Everyone, I have problems with STAR aligner. I want to use the quantMode option in order to ha [...]

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 [...]

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

UTAP – user-friendly transcriptome analysis pipeline

RNA sequencing reveals microRNA-like RNAs in fungi

Comparison of RNA-Seq data alignment and qene expression quantification tools for clinical breast cancer research

GSEPD – a Bioconductor package for RNA-seq gene set enrichment and projection display

1CellBio Announces Custom Targeted Bead Program to Accelerate Next Phase in Single-Cell Analysis

Jobs

Seeking Postdoc – Knowledge of de novo genome assembly, transcriptomics analysis (RNA-seq and others), coding in Python, Perl, and/or R

Featured RNA-Seq Job – Inside Sales / Technical Customer Service

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

Industry News

Agilent introduces new RNA / DNA QC system for NGS samples

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

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

UTAP – user-friendly transcriptome analysis pipeline

RNA sequencing reveals microRNA-like RNAs in fungi

Comparison of RNA-Seq data alignment and qene expression quantification tools for clinical breast cancer research

GSEPD – a Bioconductor package for RNA-seq gene set enrichment and projection display

1CellBio Announces Custom Targeted Bead Program to Accelerate Next Phase in Single-Cell Analysis

LIONESS – estimating sample-specific regulatory networks

RNA-Seq enables discovery of ‘kingpin’ stem cells, greater understanding of cancerous tumours

TSEE – an elastic embedding method to visualize the dynamic gene expression patterns of time series single-cell RNA sequencing data