RNA-Seq Blog

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The history of spatial transcriptomics

The function of many biological systems, such as embryos, liver lobules, intestinal villi, and tumors depends on the spatial organization of their cells. In the past decade high-throughput technologies...

MagBio Genomics Inc. develops automated RNA purification chemistry

2 days ago Leave a comment 160 Views

Mawi DNA Technologies, a biotechnology company focusing on the development of innovative technologies for biosampling, announces that MagBio Genomics has successfully developed an automated RNA purification method for iSWAB-RNA v2 ...

Mindera raises over $12M to commercialize an RNA sequencing based skin test

2 days ago Leave a comment 161 Views

Mindera Corporation today announced a $12.6M Series A-2 capital raise. The round was led by Mountain Group Partners, Rockmont Investments, and Scientific Health Development. The funding will be used to commercialize Mind.Px, ...

A robust method of nuclei isolation for single-cell RNA sequencing of solid plant tissues

2 days ago Leave a comment 310 Views

Single-cell transcriptome analysis has been extensively applied in humans and animal models to uncover gene expression heterogeneity between...

Zymo Research releases bioinformatics pipeline for SARS-CoV-2 variant detection

2 days ago Leave a comment 287 Views

Zymo Research has released the VirSieve™ Bioinformatics Pipeline source code to the environmental microbiology community to promote global collaboration and support for the detection of SARS-CoV-2 variants in wastewater. VirSieve™ ...

Integrating barcoded neuroanatomy with spatial transcriptional profiling

4 days ago Leave a comment 423 Views

There are billions of neurons in the human brain, and scientists want to know how they are connected. Cold Spring Harbor Laboratory (CSHL) Professor of Neurosciences Anthony Zador, and colleagues Xiaoyin Chen and Yu-Chi Sun, published a...

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Jobs

Post-doctoral position in computational biology of glioma

14 days ago Leave a comment 373 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: ...
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Post-doc position available – transcriptome bioinformatics and RNA sequencing

April 12, 2021 Leave a comment 684 Views
Featured RNA-Seq Job – Bioinformatician I-II

March 30, 2021 Leave a comment 781 Views
Seeking experienced research technician – single cell sequencing

March 18, 2021 Leave a comment 865 Views
Featured RNA-Seq Job – Assistant Professor – RNA Computational Biology

March 15, 2021 Leave a comment 931 Views

Industry News

MagBio Genomics Inc. develops automated RNA purification chemistry

2 days ago Leave a comment 160 Views

Mawi DNA Technologies, a biotechnology company focusing on the development of innovative technologies for biosampling, announces that MagBio Genomics has successfully developed an automated RNA purification method for iSWAB-RNA v2 ...
Read More »
Mindera raises over $12M to commercialize an RNA sequencing based skin test

2 days ago Leave a comment 161 Views
Zymo Research releases bioinformatics pipeline for SARS-CoV-2 variant detection

2 days ago Leave a comment 287 Views
Genedata Selector software ads new functionality for single-cell RNA sequencing

15 days ago Leave a comment 324 Views
ROSALIND, HELiXrUS and Geninus partner to bring powerful new single cell analysis services to cancer researchers

24 days ago Leave a comment 586 Views

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Calculating most abundant transcript from RNA-Seq data

vcf2maf uses VEP to annotate variants, and I believe selects the default Ensembl transcript to use for annotation. Sometimes the… [...]

Get Salmon mapping/alignment summary

With HISAT2, after the alignment of fastq files you get an alignment summary like this: 20000 reads; of these: 20000… [...]

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 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… [...]