RNA-Seq Blog

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RNA-Seq data suggests that exitron splicing represents an additional cancer-driving mechanism beyond genetic alterations

Northwestern Medicine studies are improving the understanding of epigenetic mechanisms in cancer development and progression, as well as pinpointing...

SPEAQeasy – a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

2 days ago Leave a comment 203 Views

RNA sequencing (RNA-seq) is a common and widespread biological assay, and an increasing amount of data is generated with it. In practice, there are a large number of individual steps ...

ac4C-seq – quantitative nucleotide resolution profiling of RNA cytidine acetylation

3 days ago Leave a comment 254 Views

A prerequisite to defining the transcriptome-wide functions of RNA modifications is the ability to accurately determine their location. NCI researchers have developed N4-acetylcytidine (ac4C) sequencing (ac4C-seq), a protocol for the quantitative single...

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

3 days ago Leave a comment 287 Views

Trips-Viz is an interactive platform for the analysis and visualization of ribosome profiling (Ribo-Seq) and shotgun RNA sequencing (RNA-seq) data...

IsoSeek – unbiased and UMI-informed sequencing of cell-free miRNAs at single-nucleotide resolution

4 days ago Leave a comment 432 Views

Terminal nucleotidyl transferases are enzymes that add non-templated nucleotides to RNA molecules. In the case of microRNAs, this process was shown to be functionally relevant for their maturation process...

Cell-level metadata are indispensable for documenting single-cell RNA sequencing datasets

4 days ago Leave a comment 348 Views

Single-cell RNA sequencing (scRNA-seq) provides an unprecedented view of cellular diversity of biological systems. However, researchers from University of Colorado School of Medicine estimate that, across the...

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Jobs

Post-doctoral position in computational biology of glioma

9 days ago Leave a comment 325 Views

To be part of the NORLUX Neuro-Oncology laboratory (Group leaders: Prof Simone Niclou and Dr. Anna Golebiewska) within the Department of Oncology at the LIH, we are currently looking for: ...
Read More »
Post-doc position available – transcriptome bioinformatics and RNA sequencing

27 days ago Leave a comment 629 Views
Featured RNA-Seq Job – Bioinformatician I-II

March 30, 2021 Leave a comment 716 Views
Seeking experienced research technician – single cell sequencing

March 18, 2021 Leave a comment 807 Views
Featured RNA-Seq Job – Assistant Professor – RNA Computational Biology

March 15, 2021 Leave a comment 875 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Base abbreviations other than ACTGU in sequence file

Short question: where can I find what F and J and [...]

What is the meaning of split read?

I want to use rna seq data to later perform functional tests on fusion genes. so before that I need… [...]

What are common ways to calculate gene length for TPM calculations? [duplicate]

I am aware of this similar question. But the accepted answer there answers how to calculate TPM given a mapping… [...]

RNAseq DE comparison with samples of different read length [duplicate]

I have RNA samples but with different read lengths (Eg, HiSeq 2x125 and NovaSeq 2x150bp data). I would like to… [...]

Normalize RNA seq data from multiple runs for expression analysis

I have RNA samples sequenced with TruSeq Stranded Total RNA kit protocol in Illumina HiSeq (2x125bp) and NovaSeq platforms (2x150bp)… [...]

correlation coefficient versus DEGs analysis: what's the best approach for low expressed genes?

I have 6 folders. Each one contains 7 datasets of a specific type of cancer (RNA-Seq) and 7 datasets of… [...]

Data format for pathway based clustering of samples

I came across this paper as one of the examples from this paper, this one Figure 2. Host Protein Alterations… [...]

Differential gene expression analysis of time series with replicates

I have a dataset that has two groups, perturbed vs control. Each group has 3 replicates. Each replicate has 8… [...]

Why did expression based subtypng of breast cancer gain much more acceptance than others

This is may not be entirely technical question but rather a academic question. But the technique behind the application is… [...]

Toptable error, wont recognize condition

I am getting a rather strange error from topTable. When I run my code I get Error in fit$coefficients[, coef]… [...]

Challenging benchmarks for supervised learning on sparse scRNA-seq data

One challenging aspect of modeling scRNA-seq data is data sparsity, that is, scRNA-seq measurements typically suffer from large fractions of… [...]

Demultiplexing FASTQ file without index information

I am trying to understand how data that was uploaded to SRA (https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=4510743) can be analyzed with the assumption that… [...]

RNASeq analysis using featureCount and EdgeR

I am using a pipeline (bam -> featurecount-> EdgeR) to do some RNASeq analysis of several groups and sub-groups. For… [...]

Un-normalize DESeq2 counts

I obtained a matrix of RNA-seq count data that has been normalized by DESeq2's median of ratio method. I know… [...]

Calculate genome coverage and depth from alignment

I have a .bam alignment file and a genome reference .fasta file. I am looking for a easy to use… [...]

Common gene naming conventions and how to convert between them

I have two questions, one is a direct question about some RNA expression data. The other is more broad, but… [...]

Doubt about using TPM for statistics

We designed an experiment to explore the potential role of carbon dioxide on algae physiology using RNA-Seq. We analyse the… [...]

Determining what RNAseq data is filtered on volcano plot

I am using RNA seq data to analyze genes via a volcano plot comparing differential gene expression of bacteria with… [...]

How to use combat in order to remove batch effects?

I have RNA seq data and I need to use combat to remove the batch effects. Somehow when I run… [...]

Fastq: how can I check if they are from DNA or RNAseq data?

I have (gave me) Illumina fastq files and I do not know if they are DNAseq or RNAseq data. How… [...]

How Do I Map, Align, And Plot My Solid Results?

Hi, I recently performed an RNA immunoprecipitation followed by SOLiD sequencing (50 bp fragmented reads). I haven't received my first… [...]

Rna Data Sources???...Please Help

hi all, I would like to have your comments on data source for RNA secondary structures at CRW site http://www.rna.ccbb.utexas.edu/… [...]

Sam Format Parsing / Stats

I will need to create summaries for a bunch of SAM files produced by Tophat (RNA-Seq spliced mapping). Are there… [...]

Rna-Seq Pipeline

So, there're papers on designing an RNA-seq experiment, and normalizing the data (Bullard et. al and the recent Genetics paper… [...]

Rna-Seq Biological Replicates...

We wish to replace microarrays with RNA-seq..we've seen papers published that specify that technical quality is quite repeatable, and thus… [...]

Rip-Seq: How Do You Determine What'S Good Coverage?

Hi I've performed an RNA-immunoprecipitation and then sequenced the results using NGS. We already have the reads mapped (s. cerevisiae),… [...]

454 Normalization

Hi I have 454 results. I have list of contigs and number of reads for each time point. I need… [...]

Peak Detection In Intergenic Regions In Rna-Seq Data

I am currently working on RNA-seq data. One of the aims is to scan intergenic regions for transcription of e.g.… [...]

Best Spliced Aligner To Human Genome With Limited Rna-Seq Reads

I'm trying to perform a spliced alignment on a limited ( [...]

Identified Potential Non-Coding Rna, And Then?

Assume we identify - by RNA-seq, tiling arrays, by prediction - possible candidate regions for non-coding, small RNAs. I wish… [...]

Searching For Specific Protein Domains In Rna-Seq

Hello, I'm trying to find specific protein domains in RNA-Seq contigs to identify previously unknown isotypes. The tool which seems… [...]

Rna-Seq Polymorphism Detection In Non-Model Plant Organism

10 individuals (samples) will be pooled and normalized into a single library for transcriptome sequencing. The reads will be paired-end… [...]

Multiplexed Rnaseq

So now that Illumina HiSeq can produce a gazillion bp of sequence per lane, what's the deal with multiplexing RNA… [...]

Finding Rrna Genes In Metagenomic Data

Hi all, I have 454 based metagenomic reads. I want to search for all ribosomal RNA in it is. So… [...]

Technical/Biological Replicates In Rna-Seq For Two Cell Lines

I have a question around the meaning of "biological replicate" in the context of applying RNA-seq to compare two cell… [...]

What'S The Difference Between 18S Rrna And 18S Rdna?

The 18S rRNA is frequently used in phylogeny (see http://en.wikipedia.org/wiki/18S_ribosomal_RNA). For example, GenBank ref. AY742884 (which I accessed from here)… [...]

Snp Analysis In 454 Sequences

Hi! I need a software to find SNPs in sequences obtained with 454 sequencing (RNA-seq). Which software would you suggest?… [...]

Multiplexed Pair-End Sequences -- Barcode Sorting

Does there exist any tool to do barcode splitting of pair-end sequences? I realise that FastX toolkit has a barcode… [...]

How To Find All Rna Stems In Genomic Data?

I am searching for RNA stems of approx. 10 to 1000 bases. Is there a fast, BLAST-like tool for scanning… [...]

Data Base Rna Seq Data

Hello, I am searching some RNA seq data for some while without success. Could you give me a hint where… [...]

Featured Presentations

The Concepts of Mean Fragment Length and Effective Length in RNA Sequencing

10 days ago

BrainSABER v0.99.5: transcriptomic similarity assessment toolkit and web application for the BrainSpan developmental dataset analysis

13 days ago

RNA-Seq Blog Transcriptome Research & Industry News

RNA-SEQ NEWS

RNA-Seq data suggests that exitron splicing represents an additional cancer-driving mechanism beyond genetic alterations

SPEAQeasy – a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

ac4C-seq – quantitative nucleotide resolution profiling of RNA cytidine acetylation

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

IsoSeek – unbiased and UMI-informed sequencing of cell-free miRNAs at single-nucleotide resolution

Cell-level metadata are indispensable for documenting single-cell RNA sequencing datasets

Jobs

Post-doctoral position in computational biology of glioma

Post-doc position available – transcriptome bioinformatics and RNA sequencing

Featured RNA-Seq Job – Bioinformatician I-II

Seeking experienced research technician – single cell sequencing

Featured RNA-Seq Job – Assistant Professor – RNA Computational Biology

Industry News

Genedata Selector software ads new functionality for single-cell RNA sequencing

ROSALIND, HELiXrUS and Geninus partner to bring powerful new single cell analysis services to cancer researchers

10x Genomics puts single cell analysis within reach of all with low throughput gene expression kit

FDA emergency use authorized for first hybridization capture-based next-generation sequencing SARS-CoV-2 RNA assay

InteRNA Technologies publishes preclinical RNA sequencing data from investigational microRNA INT-1B3 program

Featured Presentations

The Concepts of Mean Fragment Length and Effective Length in RNA Sequencing

BrainSABER v0.99.5: transcriptomic similarity assessment toolkit and web application for the BrainSpan developmental dataset analysis

Introduction to scRNA-Seq Analysis

Tutorial – RNA-Seq Analysis

Demystifying pulmonary fibrosis with single cell RNA sequencing

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

RNA-Seq data suggests that exitron splicing represents an additional cancer-driving mechanism beyond genetic alterations

SPEAQeasy – a scalable pipeline for expression analysis and quantification for R/bioconductor-powered RNA-seq analyses

ac4C-seq – quantitative nucleotide resolution profiling of RNA cytidine acetylation

Trips-Viz: an environment for the analysis of public and user-generated ribosome profiling data

IsoSeek – unbiased and UMI-informed sequencing of cell-free miRNAs at single-nucleotide resolution

Cell-level metadata are indispensable for documenting single-cell RNA sequencing datasets

Strategies for detecting and identifying biological signals amidst the variation commonly found in RNA sequencing data