RNA-Seq Blog - Part 10

RNA-SEQ NEWS

Magnetic hydrogel particles improve nanopore sequencing of SARS-CoV-2 and other respiratory viruses

February 9, 2023 Leave a comment 370 Views

Researchers from Ceres Nanosciences present a magnetic hydrogel particle enabled workflow for capturing and concentrating SARS-CoV-2 from diagnostic remnant swab samples that significantly...

FBI, SeqLL to study the forensic capabilities of direct RNA sequencing using the True Single Molecule Sequencing (tSMS®) platform

February 9, 2023 Leave a comment 536 Views

SeqLL Inc., a technology company providing life sciences instrumentation and research services, today announced the establishment of a two-year Cooperative Research and Development Agreement (CRADA) with the U.S. Department of ...

Ribo-uORF – a comprehensive data resource of upstream open reading frames (uORFs) based on ribosome profiling

February 8, 2023 Leave a comment 481 Views

Upstream open reading frames (uORFs) are typically defined as translation sites located within the 5′ untranslated region upstream of the main protein coding sequence (CDS) of messenger RNAs (mRNAs)...

DCoNA – a tool for fast differential correlation network analysis

February 7, 2023 Leave a comment 1,289 Views

One of the standard methods of high-throughput RNA sequencing analysis is differential expression. However, it does not detect changes in molecular regulation. In contrast to the standard differential...

SpliceVault – predicting the precise nature of variant-associated mis-splicing

February 7, 2023 Leave a comment 657 Views

Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity...

High-throughput droplet-based analysis of influenza A virus genetic reassortment by single-virus RNA sequencing

February 6, 2023 Leave a comment 499 Views

The segmented RNA genome of influenza A viruses (IAVs) enables viral evolution through genetic reassortment after multiple IAVs coinfect the same cell, leading to viruses harboring combinations of...

The way genes are switched on in one-cell embryos may resemble the trigger for cancer

February 6, 2023 Leave a comment 361 Views

Bath embryologists find that after fertilisation, mouse embryo genes are switched on in a pre-set order and that the triggers responsible are linked...

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Jobs

Internship / Master student in single-cell RNA-seq-based expression visualization

12 days ago Leave a comment 390 Views

You will develop and use state-of-the-art data analysis and visualization methods to extract and share single-cell RNA-seq derived gene expression...
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Featured RNA-Seq Job – Bioinformatics Scientist

14 days ago Leave a comment 326 Views
Featured RNA-Seq Job – Research Technician II – Single Cell RNA Sequencing

January 27, 2023 Leave a comment 532 Views
Post-doc position available – Bioinformatics

December 9, 2022 Leave a comment 2,629 Views
Featured RNA-Seq Job – CCG Single-Cell/-Nucleus Sequencing Group Leader, Scientist II

December 6, 2022 Leave a comment 2,396 Views

Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

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

I'm trying to re-analyse scRNA-seq data from a recently published manuscript. The methods state that the data was generated using… [...]

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 to remove double '/' from file path, bash script

I'm using the following script to detect strandedness of my paired end RNA-seq data. #!/usr/bin/env bash cd ~/Desktop/fastq for infile… [...]

How to run how_are_we_stranded_here?

I'm trying to run the python library called how_are_we_stranded_here. I have installed with pip install how_are_we_stranded_here. I have also installed… [...]

How do I determine read length from a user-inputted fastq file and then input that information into a tool's command line?

Can you guide me on how could take an input fastq file, read the length from read and then feed… [...]

How to make unrooted tree for Likelihood mapping result by using IQ2-tree?

I am a biologist, and I do not fully understand the tree topology of the experimental species. I used four-taxon… [...]

What are the conditions to perform Gene Expression Analysis on data you've performed RNA Sequence Analysis on?

I want to perform Differential Gene Expression Analysis. I recently completed RNA Sequence Analysis using the Seraut Tutorial up to… [...]

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… [...]