RNA-Seq Blog - Part 630

RNA-SEQ NEWS

Upcoming Methods Workshop – Statistical and Computational Analysis of RNA-seq Data and Its Applications

March 28, 2014 Leave a comment 4,860 Views

Session Title: Statistical and Computational Analysis of RNAseq Data and Its Applications Session Type: Methods Workshop Session Start/End Time: Saturday, Apr 05, 2014, 10:15 AM -12:15 PM Location: Room 5, ...

piClust: A density based piRNA clustering algorithm

March 28, 2014 1 Comment 7,679 Views

Piwi-interacting RNAs (piRNAs) are recently discovered, endogenous small non-coding RNAs. piRNAs protect the genome from invasive transposable elements (TE) and sustain integrity of the genome in germ cell lineages. Small ...

FANTOM5 releases atlas of human gene expression

March 28, 2014 Leave a comment 6,962 Views

FANTOM, a large international consortium led by RIKEN releases today the first comprehensive map of gene activity across the human body, and provides the first holistic view of the complex ...

Bina rebrands offerings, claims the fastest available solution for RNA-seq analysis

March 28, 2014 Leave a comment 3,516 Views

from BioIT World by Allison Proffitt March 25, 2014 | Bina Technologies announced the details of their new desktop offering this morning, along with a rebranding of their products. Last month, Bina’s ...

INsPeCT: INtegrative Platform for Cancer Transcriptomics

March 27, 2014 Leave a comment 4,643 Views

The emergence of transcriptomics, fuelled by high-throughput sequencing technologies, has changed the nature of cancer research and resulted in a massive accumulation of data. Computational analysis, integration, and data visualization ...

Long non-coding RNAs in lung cancer: comparison of microarray and RNA-seq techniques

March 27, 2014 Leave a comment 3,853 Views

from F1000 Posters PV Nazarov*, T Kaoma, A Muller, S Fritah, L Vallar *Corresponding author: PV Nazarov Genomics Research Unit, CRP-Sante, Luxembourg, Luxembourg F1000Posters 2013, 4: 1446 (poster) [English] Poster ...

In Search of RNA Epigenetics: A Grand Challenge

March 27, 2014 Leave a comment 4,123 Views

from Zone in with Zon by Jerry Zon Methylated riboA and riboC are the most commonly detected nucleobases in epigenetics research Powerful new analytical methods are key tools for progress ...

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Jobs

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

3 days ago Leave a comment 328 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...
Read More »
Post-doc positions available – Functional RNAomics

23 days ago Leave a comment 392 Views
Positions for Postdoc/Research Staff/PhD student interested in single-cell transcriptomics at the Stony Brook University

October 19, 2021 Leave a comment 1,008 Views
Featured RNA-Seq Job – Computational Scientist

October 7, 2021 Leave a comment 965 Views
Postdoc Position Available – Neurosurgery

September 22, 2021 Leave a comment 900 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Why use shuffled input-sequences as background of MOTIF discovery? (from CLIP-seq data using MEME-suite)

By default, STREME (MEME-suite) uses second-order shuffles of the input sequences as background. STREME highlights its usefulness for CLIP-data, which… [...]

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… [...]

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),… [...]