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Microwell-seq – high-throughput screening with single-cell transcriptional profiling

The research team led by Prof. GUO Guoji at the Center for Stem Cell and Regenerative Medicine, the Zhejiang University School of Basic Medical Sciences, published a research article entitled “High-throughput Microwell-seq ...

Postdoc position available – computational biology: tumour heterogeneity and resistance mechanisms

5 hours ago Leave a comment 89 Views

We are currently looking for a Post-doctoral Researcher to be part of the interdisciplinary project between NORLUX Neuro-Oncology laboratory (PIs: Dr Anna Golebiewska, Prof Simone Niclou) and Multiomics Data Analysis ...

CellHeap – a workflow for optimizing COVID-19 single-cell RNA-Seq data processing

1 day ago Leave a comment 377 Views

Currently, several hundreds of Terabytes of COVID-19 single-cell RNA-seq (scRNA-seq) data are available in public repositories. This data refers...

Automation enables high-throughput and reproducible single-cell transcriptomics library preparation

1 day ago Leave a comment 512 Views

Next-generation sequencing (NGS) has revolutionized genomics, decreasing sequencing costs and allowing researchers to draw correlations between diseases and DNA or RNA changes...

A virtual reality platform to visualize and analyze single-cell RNA sequencing data

2 days ago Leave a comment 698 Views

Science has the technology to measure the activity of every gene within a single individual cell, and just one experiment can generate thousands of cells...

Analysis workflow for publicly available RNA-sequencing datasets

2 days ago Leave a comment 594 Views

Differential gene expression analysis is widely used to study changes in gene expression profiles between two or more groups of samples (e.g., physiological versus pathological conditions...

circFL-seq – identification and quantification of full-length circRNAs for large-scale screening of functional circRNAs

7 days ago Leave a comment 491 Views

Circular RNAs (circRNAs) act through multiple mechanisms via their sequence features to fine-tune gene expression networks. Due to overlapping sequences with linear cognates, identifying internal...

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Jobs

Postdoc position available – computational biology: tumour heterogeneity and resistance mechanisms

5 hours ago Leave a comment 89 Views

We are currently looking for a Post-doctoral Researcher to be part of the interdisciplinary project between NORLUX Neuro-Oncology laboratory (PIs: Dr Anna Golebiewska, Prof Simone Niclou) and Multiomics Data Analysis ...
Read More »
Post-doc positions available – Functional RNAomics

20 days ago Leave a comment 372 Views
Positions for Postdoc/Research Staff/PhD student interested in single-cell transcriptomics at the Stony Brook University

October 19, 2021 Leave a comment 982 Views
Featured RNA-Seq Job – Computational Scientist

October 7, 2021 Leave a comment 943 Views
Postdoc Position Available – Neurosurgery

September 22, 2021 Leave a comment 883 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Why does BWA MEM orientation contradict my library prep method

I have some RNA-seq data from a stranded paired end library prep, with dUTP and UDG preparation, so the orientation… [...]

how can I get expression of an inserted foreign genes?

hi we have transgenic mice with human gene inserted. if we profom rnaseq for the mice, how can we get… [...]

Gene expression changes in one condition

I want to look at an RNA-seq data-set on 1 condition to look for expressed genes. As there is only… [...]

SyntaxError after end of Snakefile code?

I am trying to run Fastqc on multiple files using Snakemake but am receiving an ambiguous SyntaxError past the last… [...]

Snakemake Fastqc: "Multiple run or shell keywords in rule run_fastqc."

I am trying to check the quality of RNA-Seq data from Illumina using fastqc in snakemake in a conda environment.… [...]

What is the meaning of multiple "cases" in GDC data files

I thought I had a good handle on the data model of GDC, but a recent query on the TARGET… [...]

Best R program to use for RNA seq analysis

After performing RNA-seq, I am left with a CSV file containing a list of genes and the amount of reads… [...]

How to simulate replicates for DGE analysis?

I am prototyping with data visualization of DGE results, and I would like to work on the analysis pipeline before… [...]

Help with performing PCA analysis on data from 3 different datasets of normalized counts data for RNA-seq experiment

So, I have limited knowledge of R but I need to do a PCA analysis of 3 different datasets of… [...]

Error to running "CIRIquant" function in CIRIquant package at python Language

"CIRIquant" is a Python package for detecting Circular RNA. I installed "CIRIquant" through the below command in terminal: pip install… [...]

Different contrasts in DESeq2

I have a treatment and control in two time points like this > design X condition time 1 CTRL_24_hrs_replicate1 control… [...]

Convert VCF file to mpileup.txt

I am working on an iterative analysis that uses orthologous pipelines that require mpileup.txt files as input for a visualization… [...]

Alternatives to CAP-miRSeq for microRNA processing

I am involved in a Drosophila transcriptomics project in which we have been obtaining RNAseq data for microRNAs as well… [...]

Why is bcl2fastq2 taking so long to calculate stats?

Our lab has been using bcl2fastq v2.20.0.422 to demultiplex RNA-seq data sequenced on an Illumina Novaseq machine on a beefy… [...]

How to perform a meta-analysis using data consisting of paired-end and single-end reads generated from Illumina and Ion Torrent?

So basically I have RNA-seq reads that were generated from Illumina and Ion Torrent platforms for yeast species. I have… [...]

Is it possible to do DEG analysis without replicates?

I have three bulk RNA-seq samples (test1, test2, test3) without replicates. And I noticed that DEG analysis tools such as… [...]

Assembling all transcripts for an individual gene? (using single sequence to seed the assembly)

Let's say I have a candidate gene and I believe that in an individual sample, the genome sequence differs from… [...]

java error when running CIRI-full.jar Merge module

I have an issue running a module trying to detect circRNA from RNAseq data. The error is a java error… [...]

A very large number of clones in BCR reportorie

I am using mixcr to convert fq.gz raw data file (single cell BCR sequencing) to txt files with the names… [...]

Counting the number of gene isoforms in a GFF3, is this method correct?

Recently I've been tasked to count the numbers of gene isoforms for each locus in a .gff3 file. I'm still… [...]

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… [...]

How Many Reads Per Sample For Rna-Seq On Abi Solid

We are about to do our first RNA-seq (ABI Solid, mouse mRNA) experiment with our local genome core. They're new… [...]

Simulating Rna-Seq Reads

I'm curious if anyone has any experience simulating RNA-seq reads for aligner comparisons? I've found a software package called flux… [...]

The Rna Genes Download

Given the species below whose genomes are fully sequenced and annotated in NCBI. I only need to obtain all the… [...]

What Metrics Are Best To Describe The "Coverage" Of Rna-Seq Data?

As far as I know, DNA sequencing coverage is simply calculated as (read count x read length / genome size).… [...]

Investigating Snps Of Unknown Significance (Uv)

Hello I have available to be the entire set of SNPs of quite a few cows (don't know the precise… [...]

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… [...]

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… [...]

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?… [...]

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)… [...]

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… [...]

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… [...]

Multiplexed Rnaseq

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

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… [...]

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… [...]

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… [...]

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

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

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.… [...]

454 Normalization

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

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),… [...]