RNA-Seq Blog

RNA-SEQ NEWS

First RNA sequencing of human retina impacts macular degeneration treatment

Assistant professor of Ophthalmology and Visual Science and of pathology Brian Hafler and his team have successfully sequenced the RNA of the human..

Researchers leverage whole transcriptome RNA sequencing and machine learning to improve lung cancer risk stratification

2 days ago Leave a comment 621 Views

Bronchoscopy for suspected lung cancer has low diagnostic sensitivity, rendering many inconclusive results. The Bronchial Genomic Classifier (BGC) was developed to help with patient management by...

Guidelines to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation

3 days ago Leave a comment 771 Views

To use next-generation sequencing technology such as RNA-seq for medical and health applications, choosing proper analysis methods for biomarker identification remains a critical challenge for most users...

RNA Sequencing data suggests that COVID-19 patients’ deaths may be due to uncontrolled host inflammatory processes rather than an active viral infection

3 days ago Leave a comment 317 Views

Coronavirus disease 2019 (COVID-19), the global pandemic caused by SARS-CoV-2, has resulted thus far in greater than 933,000 deaths worldwide; yet...

C19-SPAR-Seq – a multiplexed, NGS platform for high-throughput detection of SARS-CoV-2

3 days ago Leave a comment 293 Views

Population scale sweeps of viral pathogens, such as SARS-CoV-2, that incorporate large numbers of asymptomatic or mild symptom patients present unique challenges for public health agencies trying to manage both travel and local spread. Physical...

seekCRIT – detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

3 days ago Leave a comment 320 Views

Over the past two decades, researchers have discovered a special form of alternative splicing that produces a circular form of RNA. Although these circular RNAs (circRNAs) have garnered considerable...

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Jobs

Featured RNA-Seq Job – scRNA-seq Biocurator/Ontologist position at FlyBase

18 days ago Leave a comment 441 Views

We are seeking to recruit a new member to our team at the University of Cambridge to contribute to the FlyBase Drosophila database. If you are looking for a fulfilling, fly-related career away from the bench, and enjoy the challenge of organizing complex...
Read More »
Featured RNA-Seq Job – Scientist – Single-Cell Bioinformatics

19 days ago Leave a comment 448 Views
Bioinformatician, Post-doctoral candidate in Bioinformatics

September 11, 2020 Leave a comment 703 Views
Featured RNA-Seq Job – Informatics & Data Science

September 2, 2020 Leave a comment 855 Views
Postdoc position available – single-cell RNA sequencing to unravel renal physiology and pathophysiology

August 26, 2020 Leave a comment 799 Views

Industry News

Bioinformatics Stackexchange
SEQanswers - RNA Sequencing

Error in cor(exprs(gse), use = "c") : no complete element pairs

I'm trying to plot a heat map for a "GSE133399", I retrieved the GSE using GEOquery package and then assigned… [...]

PacBio long-reads impact in transcriptome de novo assembly?

We are strongly interested in assembly a good transcriptome of reference for a non-model organism and build a local database.… [...]

Power law distribution alpha values

I did a Pearson co-expression analysis for generating networks for my tissue-specific (chondrocytes) RNA-seq data. I used R package poweRlaw… [...]

normalizing transcript-level expression data

Generally, RNA-seq analysis tools like edgeR or DESeq2 work on gene-level data. For differential expression (or differential transcript usage), transcript-level… [...]

smallest length of reads in 3'quantseq?

I am studying about RNA seq, and especially about 3'Quantseq(tagseq, 3primeseq). I wonder if there is a cutoff for the… [...]

data visualization RNAseq : scaling data for PCA and cluster dendogram

I have count data from a RNAseq experiment (2 samples are from normal cells and 3 samples are cells with… [...]

Does rRNA depletion protocol give higher number of mapped reads in Intronic regions?

Recently, I have downloaded a publicly available dataset, which are 350 tumor samples. I see the following information from the… [...]

if I know the number of sequencing circles can I give this information to DESeq2?

I am trying to understand library normalization in DESeq2. I would like to ask the following: I know that some… [...]

Identifying nested/overlapping reading frames in nucleotide sequences

I'll start by saying I'm a total stranger to this field, so I'd love to be corrected if I misunderstood… [...]

Mapping statistics from bam file using bbtools and sambamba

Below are the statistics for RNA-seq mapped and unmapped paired-end reads to rice genome using reformat.sh from bbtools on bam… [...]

Running GSEA or comparable analysis with multiple variable interaction?

I am working with an RNA-seq dataset generated from a complex experimental design. Our main question is focused on the… [...]

Setting Contrast for DESeq2 results

This question was also asked on BioStars I am trying to recreate this heatmap. How would I compare the four… [...]

Advantages of paired-end sequencing compared to single end

One of the advantages of paired end sequencing over single end is that it doubles the amount of data. Another… [...]

Pointing Cromwell to local EBS mounted storage on AWS Batch

I'm trying to run the WDL tasks from the GTEx RNA-Seq pipeline with Cromwell using AWS Batch as a backend.… [...]

Error using htseq-count: Could not retrieve index file

I have a total RNAseq dataset that I aligned using STAR producing BAM files (sorted by coordinates). I am now… [...]

Which of the Transcriptome assembly method is best for identifying novel lncRNAs?

I'm working with human samples and I'm trying to identify novel lncRNAs from tumor samples of Prostate cancer. I'm using… [...]

Analyzing transcripts for non-coding RNA

From a RNA seq experiment we look for the counts of transcripts of tRNA but we are also interested of… [...]

How to find siRNA off-targets from RNA-seq data?

I have an RNA-seq dataset from siRNAs targeting different components of a molecular pathway. the problem is that the siRNA… [...]

the variation between treatments is less than the variation between replicates in RNA-seq data

I have a set of RNA-seq samples from targeting different proteins in a complex with siRNAs. However, the PCA plot… [...]

NO_COOR reads not in a single block at the end 0 -1

I am doing an RNA seq analysis with mouse samples. I had my reads in several lanes, so I concatenated… [...]

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RNA-Seq Blog Transcriptome Research & Industry News

RNA-SEQ NEWS

First RNA sequencing of human retina impacts macular degeneration treatment

Researchers leverage whole transcriptome RNA sequencing and machine learning to improve lung cancer risk stratification

Guidelines to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation

RNA Sequencing data suggests that COVID-19 patients’ deaths may be due to uncontrolled host inflammatory processes rather than an active viral infection

C19-SPAR-Seq – a multiplexed, NGS platform for high-throughput detection of SARS-CoV-2

seekCRIT – detecting and characterizing differentially expressed circular RNAs using high-throughput sequencing data

Jobs

Featured RNA-Seq Job – scRNA-seq Biocurator/Ontologist position at FlyBase

Featured RNA-Seq Job – Scientist – Single-Cell Bioinformatics

Bioinformatician, Post-doctoral candidate in Bioinformatics

Featured RNA-Seq Job – Informatics & Data Science

Postdoc position available – single-cell RNA sequencing to unravel renal physiology and pathophysiology

Industry News

Paragon Genomics expands portfolio of CleanPlex® SARS-CoV-2-related viral RNA NGS tests

Ceres Nanosciences receives SBIR grant to adapt its virus capture technology to portable RNA sequencing tools for improved SARS-CoV-2 surveillance

Collaboration will demonstrate the powerful advantages of transcriptomic data analysis for prediction of the response to novel cancer therapies

Agilent Announces SureSelect XT HS2 RNA Reagent Kit, a Library Prep and Target Enrichment Solution for RNA-Seq

PEARL-seq™ – systematically identify RNA-targeted small molecules

Featured Presentations

pySeqRNA – an automated Python package for RNA sequencing data analysis

Probabilistic Gene Expression Signatures for Single Cell RNA seq Data

Supervised adversarial alignment of single-cell RNA-seq data

Bioinformatics for RNA-Seq

Webinar: New and Improved RNA-Seq Workflows

Trio RNA-Seq for viral detection

Nanoscale Automation of a Full-Length RNA Sequencing Library Preparation Method on a Microfluidic Circuit

Simultaneous Proteomics and Transcriptomics – the future of single cell analysis

An introduction to single cell RNA sequencing and clinical applications

Podcast – RNA sequencing provides new diagnoses for patients with neurodevelopmental disorders

Browsing RNA-Seq Data in Ensembl

A short movie to illustrate how RNA sequencing works

First RNA sequencing of human retina impacts macular degeneration treatment

Researchers leverage whole transcriptome RNA sequencing and machine learning to improve lung cancer risk stratification

Lexogen introduces LUTHOR 3’ mRNA-Seq Library Prep Kit for ultra-low Input and single-cell sequencing

RNA-Seq: A groundbreaking tool to preventing progressive blindness due to Retinal Degeneration

Guidelines to select sensible RNA-seq pipelines for the improved accuracy, precision, and reliability of gene expression estimation

RNA Sequencing data suggests that COVID-19 patients’ deaths may be due to uncontrolled host inflammatory processes rather than an active viral infection

C19-SPAR-Seq – a multiplexed, NGS platform for high-throughput detection of SARS-CoV-2