RNA-Seq Blog - Part 4

RNA-SEQ NEWS

Analysis of single-cell rna-seq data

12 days ago Leave a comment 1,727 Views

As single-cell RNA sequencing experiments continue to advance scientific discoveries across biological disciplines, an increasing number of analysis tools and workflows for analyzing the data have been developed. In this chapter, University of Florida...

AllenDigger – spatial expression data visualization, spatial heterogeneity delineation, and single-cell registration based on the Allen Brain Atlas

13 days ago Leave a comment 458 Views

Spatial transcriptomics can be used to capture cellular spatial organization and has facilitated new insights into different biological contexts, including developmental biology, cancer, and neuroscience. However, its wide application is still hindered by...

New research identifies an inaccuracy in the single cell GENCODE gene model

13 days ago Leave a comment 493 Views

Correction of the single cell RNA sequencing GENCODE gene model enables accurate detection and study of the novel target PVRIG, advancing...

Femtosecond laser microdissection for isolation of regenerating C. elegans neurons for single-cell RNA sequencing

15 days ago Leave a comment 277 Views

Our understanding of nerve regeneration can be enhanced by delineating its underlying molecular activities at single-neuron resolution in model organisms such as Caenorhabditis elegans. Existing cell...

Spatial epigenome–transcriptome co-profiling of mammalian tissues

16 days ago Leave a comment 368 Views

Emerging spatial technologies, including spatial transcriptomics and spatial epigenomics, are becoming powerful tools for profiling of cellular states in the tissue context1-5. However, current...

A protocol for single nucleus RNA-seq from frozen skeletal muscle

16 days ago Leave a comment 419 Views

Single-cell technologies are a method of choice to obtain vast amounts of cell-specific transcriptional information under physiological and diseased states. Myogenic cells are resistant to single-cell RNA...

Single-nucleus transcriptomics reveals new understanding of how androgen therapy affects breast tissue

17 days ago Leave a comment 1,544 Views

Insights from the study of transgender men undergoing androgen therapy may help scientists learn how to use the hormone to prevent or fight a type of breast cancer that is fueled by estrogen...

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Jobs

Post-doc position available – RNA Accelerator Inflammation and Immunology

2 days ago Leave a comment 168 Views

The postdoc will gain experience in disease-relevant immunology, cutting-edge RNA sequencing-based cell profiling and in vivo modeling. The ideal candidate should have solid training in immunology and good understanding of RNA sequencing...
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Internship / Master student in single-cell RNA-seq-based expression visualization

23 days ago Leave a comment 466 Views
Featured RNA-Seq Job – Bioinformatics Scientist

25 days ago Leave a comment 406 Views
Featured RNA-Seq Job – Research Technician II – Single Cell RNA Sequencing

January 27, 2023 Leave a comment 595 Views
Post-doc position available – Bioinformatics

December 9, 2022 Leave a comment 2,714 Views

Industry News

TileDB launches cross-language access to single-cell data

3 days ago Leave a comment 223 Views

TileDB database first to implement an open data model and API specification, enabling rapid cloud-optimized analysis of large single-cell datasets TileDB, the database for any complex data and...
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Illumina launches new software to enable tertiary analysis for oncology applications, and soon rare disease

5 days ago Leave a comment 233 Views
Quantabio adds powerful bead booster chemistry to ultra-fast sparQ RNA-Seq HMR kit

11 days ago Leave a comment 218 Views
New research identifies an inaccuracy in the single cell GENCODE gene model

13 days ago Leave a comment 493 Views
PacBio To Begin Commercial Shipment of Revio Systems

25 days ago Leave a comment 536 Views

Bioinformatics Stackexchange
Biostars - RNA Sequencing

RNAseq alignment: best practices for aligning to multiple isoforms?

I have Illumina RNAseq data and would like to maximize my power to find candidate genes that are differentially expressed… [...]

How would you define a set of active genes from a bulk RNA-seq experiment in one biological sample? [duplicate]

I am trying to identify genes that are overall considered to be "actively transcribed" in my cell line of interest… [...]

Nextflow Error: failed to read header from "-"

I am trying to run my nextflow pipeline, and have gotten this error: samtools sort: failed to read header from… [...]

RNAseq: Why would using a more complete scaffold reduce DEGs?

I have a set of RNAseq data for a couple of relatively under-studied species. They're fungi, of the order Hypocreales.… [...]

Generating gene signature for sample classification and survival analysis patient cohort

This is from this paper The LSC17 score is calculated for each patient as a linear combination of GE of… [...]

How can I process fastqs generated using the inDrops protocol into a counts matrix?

Cross-posted on Biostars I'm trying to re-analyse scRNA-seq data from a recently published manuscript. The methods state that the data… [...]

Nextflow Pipeline: Unexpected Input "{"

I'm attempting to run a nextflow pipeline and have begun getting unexpected output for a few of the processes in… [...]

To find genes that don't change in RNA-seq, Deseq2 has altHypothesis="lessAbs". Is there a way to make limma do the same thing for proteomics?

I love that Deseq2 has altHypothesis="lessAbs" !!!!!!! I've used it a ton for RNA-seq. However, now I'm working with mass… [...]

Gene symbol list for all protein coding genes in mice

How can I get a csv or a list of the gene symbol names for all the protein coding genes… [...]

Inconsistent replicate numbers in RNA-seq

I have 3 groups for the RNA-seq analysis (Control, treatment A and treatment B). There are 2 replicates for control… [...]

Which candida albicans fasta and gff file should I use for alignment?

I downloaded the gff and fasta files for candida albicans from http://www.candidagenome.org. I want to use hisat2 to align some… [...]

How to calculate cell type percentage in every sample

I have a Seurat object (metadata) with the single R samples consisting of cell types and sample types columns. I… [...]

How much does Nanopore cDNA Sequencing Cost?

[this question is based on a question that was asked on Reddit] We're interested in doing whole-transcriptome cDNA sequencing of… [...]

blood contamination rna seq

I have tumor rna seq samples. I want to find out percentage of blood contamination within these samples. What is… [...]

Error while using SummarizedExperiment() in R

I'm tryig to perform RKM normalization on raw counts for RNA-Seq Data: counts_data [...]

Does the contrast matrix I have made address the question I am trying to answer?

I have the following design matrix: mm_noreps.interactions [...]

Is it possible to do homology inference across species using different kinds of NGS data?

Background: I have a list of species that I want to put through homology inference. The goal of homology inference… [...]

Examples of machine learning approaches to validate results where ground truth is lacking?

I am currently looking into some of the published methods for deconvolution of spatial transcriptomics data where each spot does… [...]

Display row and column names in R

I have plotted a heat-map with 235 rows and 570 columns which is below: how do we make clear names… [...]

Kallisto error: index input file could not be opened!

I am utilizing Kallisto in Anaconda/miniconda for RNA sequencing. I have successfully made an index; using said index to analyze… [...]

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… [...]