RNA-Seq Blog - Part 42

RNA-SEQ NEWS

Featured RNA-Seq Job – Senior Research Assistant – lead single cell RNA sequencing and TCR sequencing

February 4, 2022 Leave a comment 1,001 Views

The Bloomberg Kimmel Institute is recruiting an individual to lead single cell RNA sequencing and TCR sequencing analytics as a Senior Research Assistant. This person will be active in the data pre...

The consequences of the low RNA input on downstream identification of differentially expressed genes

February 3, 2022 Leave a comment 1,118 Views

Multipotent neural stem cells (NSCs) are found in several isolated niches of the adult mammalian brain where they have unique potential to assist in...

Altered gene expression and cell interactions involved in COPD

February 3, 2022 Leave a comment 931 Views

Researchers at Baylor College of Medicine, Yale University and other institutions have identified previously unrecognized changes in gene expression and cellular interactions in distinct cell populations...

A re-analysis of all public RNA sequencing data reveals nine new coronavirus species

February 2, 2022 Leave a comment 1,035 Views

A former UBC post-doctoral research fellow led an international research team in re-analyzing all public RNA sequencing data to uncover almost ten times...

Single cell sequencing of live mammary cells from human milk

February 2, 2022 Leave a comment 853 Views

Researchers have explored the cellular changes that occur in human mammary tissue in lactating and non-lactating women, offering insight into the relationship between pregnancy, lactation, and...

Improved gene fusion detection in childhood cancer diagnostics using RNA sequencing

February 1, 2022 Leave a comment 935 Views

Analysis of the entire tumor RNA picks up more clinically relevant genetic changes in children with cancer than traditional diagnostic methods, new...

NetSeekR: a network analysis pipeline for RNA-Seq time series data

February 1, 2022 Leave a comment 1,438 Views

Recent development of bioinformatics tools for Next Generation Sequencing data has facilitated complex analyses and prompted large scale experimental...

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Tool for cross referencing a newly found MOTIF to database of known MOTIFS

I need a tool or a function I can use in my code (R, or Python) that I can cross… [...]

How to use the contrast function in ebayes for making different comparisons

The design matrix i have is this I would like to know how to use they way its done in… [...]

How to assess quality of WGCNA module identification in blockwisemodules()

I'm exploring WGCNA for bulkRNA sequencing analysis with human subjects. I have healthy, myocarditis, and heart failure patients (which can… [...]

Gene/protein expression specific to a group in omics

I am wondering what is the significance of finding a particular protein specific to a disease or control group? when… [...]

nested samples in design DEseq2

I'm running a DEG analysis with Deseq2 by specifing the following design that includes 12 samples from 6 pts in… [...]

How to adjust by multiple variables using ComBat-Seq?

I am trying to adjust my RNA data using ComBat-Seq (from sva R package) since I realised that there are… [...]

PWM (4xM matrices) to Sequence Logo Visualizations in MATLAB or Python

Is there a MATLAB, or else Python (not R) tool for visualizing sequence Logos from probability weight matrices (PWMs)? This… [...]

How to identify genomic regions / peaks associated with enhancers (TF binding sites)? Is there a tool or a formal recipe?

I am attempting to identify DNA sequences/regions associated with enhancers in my NGS sequencing data. How can I identify (from… [...]

How to identify which isoforms of a gene are actually expressed in my data?

I am new to bioinformatics and have been assigned the task of discovering which isoforms of a certain protein-coding gene… [...]

plotting gene expression after EdgeR DE analysis using RUVg (RUVseq) covariates

I have used the empirical RUVg method (from RUVseq) to estimate the unwanted variation of my dataset (consisting of several… [...]

Extracting clusters, hierarchical clustering - bulk RNASeq

I have been attempting to extract particular clusters, given by hierarchical clustering outputs from the pheatmap function (in R). Please… [...]

Tutorial for the WGCNA: changes in heatmap colours

I am trying to reproduce the results of the R tutorial of the WGCNA package. In section I number 5,… [...]

Find enriched processes in modules obtained by WGCNA

I am doing a gene enrichment of different clusters obtained by WGCNA, but there are some of them in which… [...]

Can I Incorporate svaseq() into GSEA/GSVA analysis?

I understand GSEA/GSVA can take microarray-like expression matrix such as the output of voom() or vst(). However, I have a… [...]

Different results of spearman correlation between TPM and FPKM

TPM and FPKM of RNA-Seq data form GDC TCGA calculated based STAR were retrieved, respectively. The correlation between a specific… [...]

DeconRNASeq: Extract gene names from returned mixing proportions

This question was also asked on Biostars I am using the Bioconductor package "DeconRNASeq" to perform tissue deconvolution. Let's say… [...]

statistical test and visualization of genes present in an experiment

I have a list of genes (n = 120) that are involved in breast cancer. And I have a list… [...]

beginner RNA-seq Replicate papers

have a good R and statistical analysis background (also with machine learning). in addition, I'm a fresh biotechnology grad. I… [...]

How can I get data of single cell RNA sequence with raw count?

I am using dataset GSE85241, but I can't find the read counts of the dataset. It only provides with RPKM… [...]

Is this RNA seq data good based on the MDS plot

I am analyzing some RNA sequencing data from a collaborator where the effect of some ligands on the transcriptome is… [...]

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… [...]