RNA-Seq Blog - Part 2

RNA-SEQ NEWS

Unraveling the timeline of gene expression – a pseudotemporal trajectory analysis of single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) technologies have rapidly developed in recent years. The droplet-based single cell platforms enable the profiling of gene expression in tens of thousands of...

INVADEseq – cataloging bacterial diversity within tumor samples

7 days ago Leave a comment 600 Views

It is said in Spanish, “si no existe, créalo” or “if it does not exist, create it.” This is exactly what sometimes occurs at the Fred Hutch. When we do ...

RNA sequencing identifies genetic effects of traumatic brain injury using an artificial brain

7 days ago Leave a comment 547 Views

The severity of traumatic brain injury (TBI) has been underscored in the last decade as doctors seek to understand its role in neurological diseases like...

Researchers develop new method to identify and remove background noise from single cell data

12 days ago Leave a comment 1,119 Views

CITE-seq (cellular indexing of transcriptomes and epitopes) is an RNA sequencing-based method that simultaneously quantifies cell surface protein and...

scReadSim – a single-cell RNA-seq and ATAC-seq read simulator

12 days ago Leave a comment 724 Views

Benchmarking single-cell RNA-seq (scRNA-seq) and single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) computational tools demands simulators to...

A longitudinal single-cell atlas of treatment response in pediatric AML

14 days ago Leave a comment 953 Views

Pediatric acute myeloid leukemia (pAML) is characterized by heterogeneous cellular composition, driver alterations and prognosis. Characterization of this heterogeneity and how it affects treatment response remains understudied in pediatric patients. ...

UC Irvine researchers discover how to better support lab grown muscle cells after transplantation

14 days ago Leave a comment 226 Views

University of California, Irvine researchers have identified a gene expressed during regeneration that is critical for muscle repair. The key human skeletal...

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Jobs

Postdoc position available – single-cell gene editing and multiomics

October 24, 2023 Leave a comment 740 Views

The primary objective of this position is to help us understand the safety of CRISPR medicines by leveraging pioneering technologies. You will get the opportunity to immerse yourself in this bustling...
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Data Scientist for Bioinformatics and Computer Biology

September 12, 2023 Leave a comment 479 Views
Job available – Data Scientist for Bioinformatics and Computer Biology

August 21, 2023 Leave a comment 579 Views
Featured RNA-Seq Job – Bioinformatician-Computational Biologist

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NERVSPAN PhD position at Single Cell Discoveries

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Industry News

Bioinformatics Stackexchange
Biostars - RNA Sequencing

Kallisto RNA-seq errors because of incompatible indices when running <kallisto quant> using downloaded mouse index

I'm trying to run RNA-seq on single-end mouse RNA data (50bp reads) but have very limited RAM ( [...]

issue with rna seq analysis

I am working on RNA seq analysis and I would like to know the following things: Current Methods: downloaded genome [...]

Mitochondrial genes - TPM calculation bulk RNA-Seq

This question was also asked on Biostars I was wondering if any of you have encountered a situation for bulk [...]

How to incorporate negative controls in DESeq2

We are doing a comparison between two outcomes (positive and negative). We could not have any positive controls as we [...]

how to use CIBERSORT

I have seen in several articles, the use of CIBERSORT to calculate the proportion of immune system cells using gene [...]

HISAT2: RNA strandedness

My library is unstranded and the code I'm trying to use is this: # Run alignment with unstranded method hisat2 [...]

Calculating p-value and adjusted p-value for pre-normalized microarray data with fold change precalculated

I have a microarray dataset with two mutants dataset that has already been normalised, and the fold change values for [...]

how to install cibersort in R, to do deconvolution using my RNA-seq Data with public single cell data

I have RNA-seq Data from lung cancer immunotherapy patients but i don't have any single cell data from my sample, [...]

Discrepancy with featurecounts analysis using a forward stranded and reverse stranded protocol

My RNAseq analysis pipeline is as follows: fastqc (read quality is good, some overrepresentation of adaptor sequence) → trimmomatic (trimmed [...]

Cannot obtain alignment summary after running Bowtie2

I am aligning my Small RNA Seq data with Bowtie 2. Although the alignment performs well, the only information I [...]

Working with Smart-seq3 data, have some questions regarding UMI and bar coding

Most of my experience has been working with genomic data, this time I am working on data from Smart-seq3. RNA [...]

Question about umap using different numbers of pca components as initialization

I am new to the scRNA-seq field and I have been doing some experiments of visualization of UMAP using different [...]

scRNA: What are good dimensionality reduction/clustering parameters to get biologically plausible groupings?

I've got a moderately large set of PBMCs, over 1M cells. That means I can't easily do a grid search [...]

Paired end reads with different read lengths

I downloaded some raw RNA-seq reads from NCBI using the sra-toolkit (Accession numbers: SRR2053159-64). The reads were generated using ABI [...]

Using CSV files continaing scRNA-seq count data from GEO [closed]

I'm completely new to scRNA-seq analysis (and to most of Bioinformatics as well) so I apologize if this was asked [...]

What are the output files of RNA-Seq from facility?

This question was also asked on Reddit I am new in our lab and I am going to do bulk [...]

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions?

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length [...]

Applying glmnet to identify predictors for subtypes

I am new to glmnet and other ML techniques, so apologise in advance if this sounds a trivial question. However, [...]

Issue with Differential Gene expression analysis with Deseq2

I am using the Deseq2 package to perform a DE analysis on multiple factors. So, basically to perform the analysis [...]

DE analysis tool and method for non-coding features

I am currently working with the non-coding features of A. thaliana, and trying to get the DE features. Among the [...]

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 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 [...]

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 [...]

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). [...]

The Rna Genes Download

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

Study highlights the power of single-nucleus RNA sequencing and spatial transcriptomics to uncover facets of disease biology

April 20, 2023

What is Strandedness in RNA-Seq data?

April 6, 2023

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

March 16, 2023