RNA-Seq Blog - Part 694

RNA-SEQ NEWS

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

January 7, 2014 Leave a comment 7,555 Views

Sm proteins are multimeric RNA-binding factors, found in all three domains of life. Eukaryotic Sm proteins, together with their associated RNAs, form small ribonucleoprotein (RNP) complexes important in multiple aspects ...

WaferGen Bio-systems Acquires a Leading Next-Generation Sequencing (NGS) Library Preparation Business and Announces Changes to its Board of Directors

January 7, 2014 Leave a comment 4,973 Views

Acquisition propels the Company to being a major player in the NGS sample prep market FREMONT, Calif., January 7, 2014 /PRNewswire/ — WaferGen Bio-systems, Inc. (QTCQB: WGBS) announced today the ...

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

January 7, 2014 Leave a comment 5,121 Views

Priming of random hexamers in cDNA synthesis is known to show sequence bias, but in addition it has been suggested recently that mismatches in random hexamer priming could be a ...

Full-length RNA-seq from single cells using Smart-seq2

January 6, 2014 Leave a comment 28,909 Views

Emerging methods for the accurate quantification of gene expression in individual cells hold promise for revealing the extent, function and origins of cell-to-cell variability. Different high-throughput methods for single-cell RNA-seq ...

Singled out for sequencing

January 6, 2014 Leave a comment 6,215 Views

from Peking University Single-cell genome and transcriptome sequencing methods are generating a fresh wave of biological insights into development, cancer and neuroscience. Kelly Rae Chi reports. Conceiving a child is ...

Programming for Evolutionary Biology Course

January 6, 2014 Leave a comment 2,464 Views

University of Porto Third Course on Programming for Evolutionary Biology When: March 21st – April 6th 2014 Location: Leipzig, Germany Application deadline: January 15th 2014 Detailed information about the course ...

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Jobs

Featured RNA-Seq Job – Staff Bioinformatics Scientist, RNA-Seq

8 days ago Leave a comment 495 Views

For this position, we are looking for a candidate with strong experience on secondary analysis RNAseq pipelines and lead a team of bioinformatic scientists...
Read More »
Featured RNA-Seq Job – Senior Research Software Engineer

28 days ago Leave a comment 579 Views
Featured RNA-Seq Job – Computational Biology Scientist, Cancer Immunology

January 18, 2021 Leave a comment 900 Views
Associate Professor

January 17, 2021 Leave a comment 672 Views
Post-doctoral position in pharmacogenomics for glioma

January 5, 2021 Leave a comment 839 Views

Industry News

Bioinformatics Stackexchange
SEQanswers - RNA Sequencing

Explanation for RNA-seq samples not clustering in PCA as expected

A colleague is analysing RNA-seq data - the study design is 2 treatments, 3 replicates, 3 tissues. In their PCA… [...]

Trouble aligning next generation sequencing data to reference genomes using QuasR package in Bioconductor. Cannot import .txt

I'm trying to check the quality of my paired end read sequencing data. I am following this pipeline (https://f1000research.com/articles/4-1062#ref-21) which… [...]

Kallisto psudoaligner quant not giving me expected output

I am trying to run this kallisto (latest) quant and all I get are abundance and json files. kallisto quant… [...]

Clustering RNAseq fold-change data

I have a dataset that looks something like this Treatment1 Treatment 2 Control Sample1 3.23. 0.87. 1 Sample2 1.71. 1.… [...]

How do you determine the strandedness of a RNAseq dataset? [duplicate]

How do you verify if a RNAseq dataset is unstranded, stranded or revesely stranded from a fastq file? [...]

Multi Omics comparison RNA seq : Condition specific gene signature

The authors of an article are comparing different cell type and the organ type and they show the ontology enrichment… [...]

workflow for processed RNAseq data analysis in R [closed]

I'm learning to use R in data analysis. I'm getting fluent in baseR and the tidyverse, but thus far only… [...]

RNA_Seq Analysis in R, propmapped function issue

I'm currently trying to learn RNA-seq data analysis and differential expression in R. I've been using the Combine lab tutorial.… [...]

TCGA dataset: different accession IDs mapped to same location?

I'm currently working on TCGA miRNA dataset. After constructing a reads matrix, I'm trying to find the isoform sequence. In… [...]

ATAC and RNA seq Up regulated region gene and scatter

I m not sure if I'm going the right way or not but when the gene and region and both… [...]

What are the applications of DNA or RNA pattern matching?

I'm assuming we don't do pattern matching in DNA or RNA for the fun of it. So I'd like to… [...]

Clarification regarding (deepTools) bamCoverage output

Im using bamCoverage on a file and ive set the bin size to 1 but also normalizing using RPKM for… [...]

How to control/normalize for number of reads when calling SNPs using RNA-Seq?

I used the GATK pipeline to call SNPs on males and females using RNA-Seq data. But the males have a… [...]

Query on htseq count

This question has also been asked on Biostars I am trying to run htseq-count for carrying out rna-seq analysis for… [...]

What is the best way to map/align my reads on a given genome?

I am frequently using a ballgown package for my rnaseq analysis, but recently I have had a new task to… [...]

What is a sensible number of gene/observations to explain PCA variance?

I am working with a set of RNASeq dataset. I have about 4000 observations (genes) on 20 samples and plotting… [...]

Question of Padj value (very high, infinite) got from dds

After I got dds from my count matrix by DESeq(), I use results() method to get Padj and log2 fold… [...]

How would we test for significant changes in expression when many of the normalised counts are clustered together?

I've been handed RNA-seq data with a lot of associated covariates. This data has been put through the DESeq2 package… [...]

ConsensusClusterPlus for sample classification

Many large studies like TCGA use consensus clustering for transcriptional subtype identification. The most popular package for that seems to… [...]

If a gene is expressed at a level of 1/1200 compared to the average gene, how is probability 50:50 that we have a read mapped to it?

I am reading a book about RNAseq analysis and it says "To calculate the probability that a read will map… [...]

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RNA-Seq Blog Transcriptome Research & Industry News

RNA-SEQ NEWS

RIP-seq analysis of eukaryotic Sm proteins identifies three major categories of Sm-containing ribonucleoproteins

WaferGen Bio-systems Acquires a Leading Next-Generation Sequencing (NGS) Library Preparation Business and Announces Changes to its Board of Directors

Consistent Errors in First Strand cDNA Due to Random Hexamer Mispriming

Full-length RNA-seq from single cells using Smart-seq2

Singled out for sequencing

Programming for Evolutionary Biology Course

Jobs

Featured RNA-Seq Job – Staff Bioinformatics Scientist, RNA-Seq

Featured RNA-Seq Job – Senior Research Software Engineer

Featured RNA-Seq Job – Computational Biology Scientist, Cancer Immunology

Associate Professor

Post-doctoral position in pharmacogenomics for glioma

Industry News

Seven Bridges Selected by Pfizer to Support Data Management Solution for Single-Cell RNA Sequencing Data

Resolve Biosciences’ Molecular Cartography platform detects specific gene expression patterns in SARS-CoV-2 not seen with existing single-cell RNA-seq technologies

Molecular Stethoscope publishes human proof-of-concept study for its cell-free mRNA based NGS liquid biopsy technology platform

OmniSeq collaborates with UPMC to employ its RNA sequencing (RNA-seq) gene expression profile assay for selecting cancer immunotherapy combinations

Zymo Research Launches COVID-19 RNA Sequencing Service for the Detection and Surveillance of Emerging SARS-CoV-2 Variants

Featured Presentations

RNA-Seq – a closer look at read mapping

Enriching pathogen transcripts from infected samples: a capture based approach to improved host-pathogen RNA-Seq

Introduction to single cell RNA sequencing data analysis

HMS Initiative for RNA Medicine

Overview of Drop-seq technology

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

Learn more about available bioinformatics tools and pipelines to analyze RNA sequencing data

New search engine for single cell atlases

Yale researchers identify tumor reactive immune cells with RNA sequencing to help fight against advanced melanoma

New algorithm identifies ‘escaping’ cells in single-cell CRISPR screens

RNA sequencing brings hope for endangered wild cats

Mim-tRNAseq – A method that accurately measures the abundance and modification status of different tRNAs

Uncovering the Anti-Myeloma Resistance Files