RNA-Seq Blog - Part 70

RNA-SEQ NEWS

iDIRECT – disentangling direct from indirect relationships in association networks

January 14, 2022 Leave a comment 1,197 Views

Networks are vital tools for understanding and modeling interactions in complex systems in science and engineering, and direct and indirect...

small RNA sequencing suggests BPA exposure of the placenta could affect fetal brain development

January 14, 2022 Leave a comment 1,005 Views

In a new study, scientists at the University of Missouri demonstrate the direct transmission of bisphenol A (BPA) from a mother to her...

A comprehensive comparison of supervised and unsupervised methods for cell type identification in single-cell RNA-seq

January 13, 2022 Leave a comment 1,545 Views

The cell type identification is among the most important tasks in single-cell RNA-sequencing (scRNA-seq) analysis. Many in silico methods have been developed and can be roughly categorized as...

Using synthetic chromosome controls to evaluate the sequencing of difficult regions within the human genome

January 13, 2022 Leave a comment 849 Views

Next-generation sequencing (NGS) can identify mutations in the human genome that cause disease and has been widely adopted in clinical diagnosis. However, the human genome contains many...

LMU researchers have developed a method to extract more information from RNA sequencing data

January 12, 2022 Leave a comment 1,182 Views

Higher organisms store their genetic material in the nuclei of cells as deoxyribonucleic acid (DNA). In a process called transcription, individual segments, the genes, are converted into messenger ribonucleic...

Long read sequencing reveals novel isoforms and insights into splicing regulation during cell state changes

January 12, 2022 Leave a comment 1,063 Views

Alternative splicing is a key mechanism underlying cellular differentiation and a driver of complexity in mammalian neuronal tissues. However, understanding of which isoforms are differentially used or...

Lucence’s LiquidHALLMARK Sequencing-based Liquid Biopsy Assay Expands to Include cfRNA

January 12, 2022 Leave a comment 1,022 Views

Lucence, a precision oncology company using liquid biopsy to bring clarity to cancer care, is announcing the availability of an expanded version of its...

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Can Gene Expression Analysis be performed on this?

I recently derived this table manually. I'm new to bioinformatics. I'm wondering what is done after this? Can Gene Expression… [...]

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… [...]

Can I perform Expression Analysis on this 10x dataset?

10x Genomics: 20k Human PBMCs is the dataset. Description of the dataset: Inputs/Libraries Human peripheral blood mononuclear cells (PBMCs) of… [...]

Calling isoforms from long read data generated from partially degraded RNA

What will be the best tool to call isoforms from long read data generated from partially degraded RNA. By mistake… [...]

How to find closely related genes for a specific gene from WGCNA modules?

I have used WGCNA by integrating several datasets which are processed in a similar way. Identified 17 modules, followed by… [...]

Benchmarking for variant identification using RNA-seq data

I am in need to benchmark the variant identification pipeline which uses RNA seq data alone without any matched-normal. I… [...]

Ubiquitous regulation of highly specific marker genes

I am fairly new to scRNAseq analysis and keep running into the same problem in the two datasets I am… [...]

Snakemake MissingRuleException

I'm trying to run a snakefile for the first time with limited coding experience using salmon to index a reference… [...]

Number of Spots in a Spatial Seurat object

I have got an integrated seurat object of 21 Spatial samples. I want to know how many spots are in… [...]

Stringtie/DEprep.py gene/transcript IDs are wrongly formatted

Hi my RNAseq workflow is ending up with wrongly formatted gene IDs (and separately transcript _IDs) after a Hisat2 ->samtools… [...]

Is it possible to integrate multiple gene expression datasets and use it for WGCNA?

I have 8 RNA-seq datasets and am interested in looking at genes co-expressed with a specific gene. Among 8 RNA-seq… [...]

select highly variable genes out of dataframe

lets say I have the following dataframe: Ensembl_ID A B C D E F G ENSG00000236601.2 0 0 0 1… [...]

WCGNA - Relate modules with Y features when the % of variance explained of each eigengen is low

I'm doing a WCGNA analysis (signed network) on microbiome 16S data. I have transformed counts to centeres log-ratio transformed data… [...]

Avoiding false anticorrelations between individual genes per cell in single-cell RNAseq

When analysing a single-cell RNAseq dataset, one question I like to ask is: At a single-cell level, are these two… [...]

What codes represent what genes?

I want to run experiments on the data used in PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome… [...]

Is loss/gain of function reflected in RNA-seq transcript counts?

Do LoF/GoF transcripts count toward the RNA-seq TPM count? Or would these LoF/GoF transcripts only be detected by isoform quantification? [...]

How should I interpret DGE results if only one HLA-A gene shows up as significant but not the others?

I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A.… [...]

Expression analysis of miRNAs with normal RNA-seq data without small RNA-seq data

I am looking to perform expression analysis of miRNAs with normal RNA-seq data lacking small RNA-seq data? Which path should… [...]

Genome-guided transcriptome reconstruction: should I filter my reference annotation by transcript_support_level or other tags?

Is there really any advantage to filtering the GTF annotation for transcriptome reconstruction (or, for example, for pseudo-alignment quantification)? Are… [...]

GSEA. Subsetting Gene Ontology, Biological Processes, by gene set families of interest

I have run GSEA - on Gene Ontology , Biological Processes (GO and BP hereafter) - on some Mouse bulk… [...]

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… [...]