RNA-Seq Blog - Part 7

RNA-SEQ NEWS

Single cell RNA sequencing sheds light on neurodevelopmental disorders

December 14, 2021 Leave a comment 613 Views

New research from the Institute of Psychiatry, Psychology & Neuroscience (IoPPN) at King’s College London has found that some processes behind the...

RNA modifications detection by comparative Nanopore direct RNA sequencing

December 14, 2021 Leave a comment 605 Views

RNA molecules undergo a vast array of chemical post-transcriptional modifications (PTMs) that can affect their structure and interaction properties...

Measuring cancer cell state can reveal drug susceptibility

December 13, 2021 Leave a comment 659 Views

Study results also show that pancreatic tumor cells can be forced into a more susceptible state by changing their environment. Over the past few decades, scientists have made great strides ...

10th Gene Quantification Event qPCR dPCR & NGS 2022

December 13, 2021 Leave a comment 531 Views

We broaden our focus in genomics applications from quantitative RT-PCR, to digital-PCR and the latest Next-Generation Sequencing Technologies as well as the connected integrative Multi-Omics data...

CRISPRroots – on- and off-target assessment of RNA-seq data in CRISPR–Cas9 edited cells

December 10, 2021 Leave a comment 601 Views

The CRISPR-Cas9 genome editing tool is used to study genomic variants and gene knockouts, and can be combined with transcriptomic analyses to...

SPLINTR – provides insights into the non-genetic transcriptional processes that underpin malignant clonal fitness

December 10, 2021 Leave a comment 615 Views

All cancers emerge after a period of clonal selection and subsequent clonal expansion. Although the evolutionary principles imparted by genetic intratumour heterogeneity are becoming increasingly clear...

Exai Bio secures $67.5 million series A financing to advance next-generation, RNA-based liquid biopsy platform for early cancer detection

December 10, 2021 Leave a comment 577 Views

Exai Bio, a next-generation liquid biopsy company, today announced it has raised a $67.5 million Series A financing to accelerate development of its non...

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Jobs

Bioinformatics research positions available

December 16, 2021 Leave a comment 612 Views

The Bioinformatics Group in the Center for Systems Immunology is seeking Postdoctoral Fellows and multiple Bioinformatician II-III’s. These individuals will drive project teams performing RNA-seq...
Read More »
Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks

December 7, 2021 Leave a comment 330 Views
Postdoc position available – computational biology: tumour heterogeneity and resistance mechanisms

December 1, 2021 Leave a comment 640 Views
Post-doc positions available – Functional RNAomics

November 11, 2021 Leave a comment 666 Views
Positions for Postdoc/Research Staff/PhD student interested in single-cell transcriptomics at the Stony Brook University

October 19, 2021 Leave a comment 1,346 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

How to remedy a DESeq2 collapsing technical replicates error?

Goal: To ensure "the sum of the counts for [my samples] is the same as the counts in the [samples]… [...]

How can I get a column with real gene names in my ballgown analysis?

I am doing RNAseq analysis and I am using ballgown procedure for it. There is an option in R to… [...]

Should I remove days_to_death = 0 before TCGA survival analysis

Some patients in TCGA data have days_to_death = 0 and days_to_follow_up = NA vice versa. Should I remove these samples… [...]

Nextflow HISAT2 command exit status 255 with prebuild index

I have a problem with my nextflow pipeline. My workflow looks like this: Uncompress the hisat2 genotpye index grch38_genome.tar.gz from… [...]

How to find an unidentified splicing variant of a protein?

I have some data indicating there might be a splicing variant of the Arabidopsis Thaliana protein I'm studying that has… [...]

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

We have an RNA seq taken from a the same tissue in two different developmental stages. We have one gene,… [...]

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 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… [...]