Category: RNA

Reproductive Medicine Associates of New York Presents Innovative Research at ASRM’s 77th Annual Meeting

RMA of New York leads the way with ground-breaking innovative genomics and artificial intelligence research to improve patient care and IVF success rates Published: Oct. 19, 2021 at 9:00 AM MDT|Updated: 4 hours ago BALTIMORE, Md., Oct. 19, 2021 /PRNewswire/ — Physicians and scientists at Reproductive Medicine Associates of New York…

Continue Reading Reproductive Medicine Associates of New York Presents Innovative Research at ASRM’s 77th Annual Meeting

Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

Probiotic intake commonly altered the genetic composition of gut microbial residents To comprehensively understand the adaptive mutations in the resident gut microbiota due to probiotic intake, we first collected and curated publicly available metagenomic studies related to probiotics with the following criteria. (1) The study has a longitudinal design, which…

Continue Reading Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota

The Profile and Function of Gut Microbiota in Diabetic Nephropathy

Introduction Diabetic nephropathy (DN) is characterized by kidney function loss caused by diabetes mellitus.1 Almost one-third of patients with diabetes have DN, and the prevalence of DN is increasing worldwide.2 DN is one of the most important factors of chronic kidney disease and end-stage renal disease (ESRD). The signs and…

Continue Reading The Profile and Function of Gut Microbiota in Diabetic Nephropathy

Distant residues modulate conformational opening in SARS-CoV-2 spike protein

Correlation between RBD Opening and Backbone Dihedral Angle. Multiple unbiased trajectories were propagated from different regions of the S-protein RBD opening conformational space, priorly explored by SMD and umbrella sampling (details in SI Appendix). Three of those trajectories were assigned as the closed, partially open, and fully open states, based…

Continue Reading Distant residues modulate conformational opening in SARS-CoV-2 spike protein

Promega Launches Sanger Sequencing Chemistry Compatible With All Capillary Electrophoresis Platforms

ProDye™ Terminator Sequencing System brings Sanger sequencing to any size laboratory MADISON, Wis., October 19, 2021–(BUSINESS WIRE)–Research labs performing Sanger sequencing can now use Promega chemistry on any capillary electrophoresis (CE) platform. The ProDye™ Terminator Sequencing System, launched today by Promega Corporation, can be implemented on any CE instrument, including…

Continue Reading Promega Launches Sanger Sequencing Chemistry Compatible With All Capillary Electrophoresis Platforms

A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

1. Weber, S., Ramirez, C. & Doerfler, W. Signal hotspot mutations in SARS-CoV-2 genomes evolve as the virus spreads and actively replicates in different parts of the world. Virus Res. 289, 198170 (2020). CAS  PubMed  PubMed Central  Article  Google Scholar  2. Sekowska, A., Wendel, S., Fischer, E. C. & Nørholm,…

Continue Reading A mutational hotspot that determines highly repeatable evolution can be built and broken by silent genetic changes

Single cell RNA-seq analysis using a Galaxy interface

In this webinar, we will look at a Galaxy interface for single cell analysis. Specifically, we will run Scanpy (which would otherwise require Python programming skills) to analyse a Drop-seq dataset located in EMBL-EBI’s Single Cell Expression Atlas. Who is this course for? This webinar is aimed at individuals…

Continue Reading Single cell RNA-seq analysis using a Galaxy interface

Labelling SNPs in a stacked manhattan plot with karyoploteR

Labelling SNPs in a stacked manhattan plot with karyoploteR 0 When combining multiple GWAS results into a stacked manhattan plot using KaryoploteR, how do you label top SNPs in each set of GWAS results? Instructions provided for labelling a single manhattan plot did not work for the stacked manhattan. manhattan…

Continue Reading Labelling SNPs in a stacked manhattan plot with karyoploteR

cpan install Bio::PrimerDesigner

Hi, I am trying to install Bio::PrimerDesigner on ubuntu 18.0 but getting this error. “/usr/bin/perl Build.PL –installdirs site — NOT OK”. The detail logs are also mentioned below. Thanks in advance. Logs: sudo cpan install Bio::PrimerDesigner Loading internal logger. Log::Log4perl recommended for better logging Reading ‘/root/.cpan/Metadata’ Database was generated on…

Continue Reading cpan install Bio::PrimerDesigner

very different outputs from rMATS vs altanalyze

alternative splicing: very different outputs from rMATS vs altanalyze 0 We are comparing two RNA-seq datasets (read length = 150nt, depth = 50M reads, 2 conditions, n = 4 per condition) for alternative splicing. I used rMATS and altanalyze to find alternative splicing events. However, there is very little overlap…

Continue Reading very different outputs from rMATS vs altanalyze

Gmod Player X Genshin Impact (Multiplayer Edition) “Slow Update”

Name: Sky Stargazer Age: 15 Roles: Defense Likes: Fish, Choccy Milk, Coca-Cola, Terraria, Minecraft, Genshin Impact, Friday Night Funkin’, Stargazing Hates: Thots, Betrayals, Harem, Jerks, Fatui, Love Relationships Zodiac Sign: Scorpio Weapons: Crowbar, Physics Gun, Gravity Gun, TFA and Arctic 2.0 Arsenals, Reinhardt’s Hammer from Overwatch Height: 154 cm Health:…

Continue Reading Gmod Player X Genshin Impact (Multiplayer Edition) “Slow Update”

Research progress on the physiological function of mtDNA and its specific detection and therapy

doi: 10.1002/cbic.202100474. Online ahead of print. Affiliations Expand Affiliations 1 Nanjing Tech University, Institute of Advanced Materials, CHINA. 2 Northwestern Polytechnical University, Institute of Flexible Electronics, CHINA. 3 Nanjing Tech University, Institute of Advanced Materials, 30 South Puzhu Road, 210008, Nanjing, CHINA. Item in Clipboard Congcong Zhang et al. Chembiochem. 2021….

Continue Reading Research progress on the physiological function of mtDNA and its specific detection and therapy

Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

Akbari MT, Izadi P, Izadyar M, Kyriacou K, Kleanthous M (2008) Molecular basis of thalassemia intermedia in Iran. Hemoglobin 32:462–470 CAS  Article  Google Scholar  Al-Allawi NA, Jubrael JM, Hughson M (2006) Molecular characterization of β-thalassemia in the Dohuk region of Iraq. Hemoglobin 30:479–486 CAS  Article  Google Scholar  Alibakhshi R, Kianishirazi…

Continue Reading Following the Trace of HVS II Mitochondrial Region Within the Nine Iranian Ethnic Groups Based on Genetic Population Analysis

Contrast treated samples against both scramble and untreated controls

Hi there, I am using DESeq2 to analyse RNAseq from siRNA treated samples and 2 controls (Scramble and Untreated). Each treatment has 4 cell lines: treatment cellline group <fct> <fct> <fct> 1 Untreated 1 Control 2 Scramble 1 Control 3 Knockdown 1 Knockdown 4 Untreated 2 Control 5 Scramble 2…

Continue Reading Contrast treated samples against both scramble and untreated controls

Assistant Professor in Molecular or Cellular Biology and Bioinformatics

Description Assistant Professor in Molecular or Cellular Biology and Bioinformatics Apply now Job no: 510522 Position Type: Faculty Full Time Campus: UMass Boston Department: Biology Pay Grade: No Pay Grade Date opened: 18 Oct 2021 Eastern Daylight Time Applications close: The Department of Biology at the University of Massachusetts Boston…

Continue Reading Assistant Professor in Molecular or Cellular Biology and Bioinformatics

For DE analysis, should I exclude all the samples that don’t have the data of normal tissue?

For DE analysis, should I exclude all the samples that don’t have the data of normal tissue? 0 Hi I have downloaded the RNA-Seq data of my interest cancer type from TCGA. most of the samples are the primary tumor and just a few of them are the normal tissue….

Continue Reading For DE analysis, should I exclude all the samples that don’t have the data of normal tissue?

Computational Biology Trainer for VIB and ELIXIR Belgium

Description Posted Date 18 Oct 2021 Locations Ghent Center VIB Bioinformatics Core Type Bio IT Positions 1 About VIB and ELIXIR Belgium VIB is an entrepreneurial non-profit research institute with a clear focus on ground-breaking strategic basic research in life sciences and operates in close partnership with the five universities…

Continue Reading Computational Biology Trainer for VIB and ELIXIR Belgium

Is it representative to use the minimal matched data of RNA-Seq in TCGA?

Is it representative to use the minimal matched data of RNA-Seq in TCGA? 0 Hi all, As far as I understood, the number of “solid tissue normal” data in TCGA is minimal, and given this, I have two questions: For DE analysis that we need the matched data of normal…

Continue Reading Is it representative to use the minimal matched data of RNA-Seq in TCGA?

11th Place Solution of Kaggle Global Wheat Detection

Solution Summary Our solution is based on the excellent MMDetection framework. We trained an ensemble of the following models: To increase the score a single round of pseudo labelling was applied to each model. Additionally, for a much better generalization of our models, we used heavy augmentations. Jigsaw puzzles In…

Continue Reading 11th Place Solution of Kaggle Global Wheat Detection

I’m not sure my Bulk RNAseq read counts extracted from fastq file are correct

I’m not sure my Bulk RNAseq read counts extracted from fastq file are correct 1 Hi. I’m new in bioinformatics and I’m trying to extract read counts from fastq files. I used STAR alignment method with GENCODE annotation files. (I didn’t trimmed by reads because I heard that trimming is…

Continue Reading I’m not sure my Bulk RNAseq read counts extracted from fastq file are correct

use files with same name as input? : bioinformatics

Hi everyone, I have a question regarding the input of several fastq files into ‘CellRanger count’ pipeline.I performed scRNA-seq of different samples at a partner institute and the sequencing facility started by sequencing all the samples at a lower depth (to test the quality of the libraries) and only then…

Continue Reading use files with same name as input? : bioinformatics

HsMetricCollector (gatk 4.0.5.0 API)

HsMetricCollector (gatk 4.0.5.0 API) JavaScript is disabled on your browser. public class HsMetricCollector extends TargetMetricsCollector<HsMetrics> Calculates HS metrics for a given SAM or BAM file. Requires the input of a list of target intervals and a list of bait intervals. Can be invoked either on an entire iterator of SAMRecords…

Continue Reading HsMetricCollector (gatk 4.0.5.0 API)

ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files

GitHub – ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time About Wrapper script for a GenePattern module to create a velocity compatible loom file…

Continue Reading ACastanza/SingleCell.BAM.to.Velocity: Wrapper script for a GenePattern module to create a velocity compatible loom file from single cell bam files

How to make tests for the RNA-Seq, proteomic, clinical data

How to make tests for the RNA-Seq, proteomic, clinical data 0 Generally, there are thousands of genes/proteins/clinical with several samples per group in the RNA-Seq or proteomic data. Should I test the normal distribution per gene per group (plan A) or using all the data (such as a matrix containing…

Continue Reading How to make tests for the RNA-Seq, proteomic, clinical data

Bristol Myers Squibb hiring Senior Scientist, Translational Bioinformatics in Princeton, New Jersey, United States

At Bristol Myers Squibb, we are inspired by a single vision – transforming patients’ lives through science. In oncology, hematology, immunology and cardiovascular disease – and one of the most diverse and promising pipelines in the industry – each of our passionate colleagues contribute to innovations that drive meaningful change….

Continue Reading Bristol Myers Squibb hiring Senior Scientist, Translational Bioinformatics in Princeton, New Jersey, United States

In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?

In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger? 0 In single cell RNA-seq, do we perform regular quality checks and adapter trimming (just like in regular RNA-seq) before using cellranger? cellranger adapter_trimming QC scRNA-seq • 10 views • link 2 hours ago…

Continue Reading In single cell RNA-seq, do we perform regular quality checks and adapter trimming before using cellranger?

Gromacs manual grompp

#725013 – gromacs-openmpi: grompp crashes with invalid GROMACS Molecular Dynamics & GPU Acceleration | NVIDIA Instead, frustrated and confused. The man was slumped over, but he absorbed the blow and stumbled back. But I think it will be better used in this situation.He stopped at my open window to address…

Continue Reading Gromacs manual grompp

Technical Support Specialist – BioInformatics – Invitae

POSITION SUMMARYThe Technical Support Specialist provides first level technical support on Invitae Somatic Oncology products from the Invitae office in Boulder, CO. This individual will escalate customer inquiries effectively, collect customer feedback and share this with internal teams to improve products. This individual will assist in coordinating activities for special…

Continue Reading Technical Support Specialist – BioInformatics – Invitae

CrossMap issues changing genome version

CrossMap issues changing genome version 0 I installed CrossMap for conversion of bam, bed, gtf files from one version to another. I use GENCODE so I need to make the files compatible with UCSC browser. I am running into two issues with this tool… If I use following command to…

Continue Reading CrossMap issues changing genome version

Does hisat2 –rg flag eat the “/” character in multiline definitions?

Does hisat2 –rg flag eat the “/” character in multiline definitions? 0 Hello, I am trying to use hisat2, but I noticed something weird. When running it like so: hisat2 -p 8 –rg-id=UHR_Rep2 –rg SM:UHR –rg LB:UHR_Rep2_ERCC-Mix1 –rg PL:ILLUMINA –rg PU:CXX1234-TGACAC.1 -x $RNA_REF_INDEX –dta –rna-strandness RF -1 “$RNA_DATA_DIR/${SAMPLE}_1.fastq.gz” -2 “$RNA_DATA_DIR/${SAMPLE}_2.fastq.gz”…

Continue Reading Does hisat2 –rg flag eat the “/” character in multiline definitions?

Technical Support Specialist – BioInformatics – Invitae (Formerly ArcherDx)

POSITION SUMMARYThe Technical Support Specialist provides first level technical support on Invitae Somatic Oncology products from the Invitae office in Boulder, CO. This individual will escalate customer inquiries effectively, collect customer feedback and share this with internal teams to improve products. This individual will assist in coordinating activities for special…

Continue Reading Technical Support Specialist – BioInformatics – Invitae (Formerly ArcherDx)

Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse

The removal of problematic regions The removal of problematic genomic regions is considered essential for the accurate analysis of data obtained by chromatin immunoprecipitation followed by genome sequencing (ChIP-Seq) [27, 35]. Repetitive regions including satellite DNA arrays comprise a majority of such problematic regions, mainly because they reside in the…

Continue Reading Differential enrichment of H3K9me3 at annotated satellite DNA repeats in human cell lines and during fetal development in mouse

KEGG ENZYME: 1.1.1.124

KEGG ENZYME: 1.1.1.124     ENZYME: 1.1.1.124 Help Entry EC 1.1.1.124                Enzyme                                  Name fructose 5-dehydrogenase (NADP+);5-ketofructose reductase (NADP+);5-keto-D-fructose reductase (NADP+);fructose 5-(nicotinamide adenine dinucleotide phosphate) dehydrogenase;D-(-)fructose:(NADP+) 5-oxidoreductase;fructose 5-dehydrogenase (NADP+) Class Oxidoreductases;Acting on the CH-OH group of donors;With NAD+ or NADP+ as acceptorBRITE hierarchy Sysname D-fructose:NADP+ 5-oxidoreductase Reaction(IUBMB) D-fructose + NADP+ = 5-dehydro-D-fructose + NADPH…

Continue Reading KEGG ENZYME: 1.1.1.124

GEO scRNA-seq entry with cell type information?

GEO scRNA-seq entry with cell type information? 1 Hello, I am trying to look for a scRNA-seq dataset hosted in GEO that, apart of the common files genes.tsv, barcodes.tsv and matrix.mtx, also has a file mapping barcode to cell types (as annotated by the paper). I have been trying to…

Continue Reading GEO scRNA-seq entry with cell type information?

How to perform sequence quality filtering of raw reads for single cell RNA seq?

How to perform sequence quality filtering of raw reads for single cell RNA seq? 0 I have a few single-cell RNA-seq samples (raw fastq reads). When I process raw reads, what should I do first? Is it demultiplexing? If so, what is the best tool I can use? Can I…

Continue Reading How to perform sequence quality filtering of raw reads for single cell RNA seq?

GTF upload error UCSC related to stradedness

GTF upload error UCSC related to stradedness 0 Hello, I’m having issues with uploading a .gtf file to the UCSC browser. I am getting the following error: “Error GFF/GTF group STRG.155047.1 on chr12+, this line is on chr12-, all group members must be on same seq and strand” I have…

Continue Reading GTF upload error UCSC related to stradedness

use files with same name as input

Cell Ranger count pipeline: use files with same name as input 0 Hello, I have a question regarding the input of several fastq files into ‘CellRanger count’ pipeline. I performed scRNA-seq of different samples at a partner institute and the sequencing facility started by sequencing all the samples at a…

Continue Reading use files with same name as input

help with time series analysis

help with time series analysis 0 Hello, I have readcount data from my metagenome experiment. My metagenome experiment looks like this: control T0 T1 T2 T3 T4 case T0 T1 T2 T3 T4 I have two conditions (case and control) and five time points. I have readcounts data from each…

Continue Reading help with time series analysis

Runs of homozygosity in Plink

❯ plink1.9 –homozyg –help PLINK v1.90b6.22 64-bit (3 Nov 2020) www.cog-genomics.org/plink/1.9/ (C) 2005-2020 Shaun Purcell, Christopher Chang GNU General Public License v3 –help present, ignoring other flags. –homozyg [{group | group-verbose}] [‘consensus-match’] [‘extend’] [‘subtract-1-from-lengths’] –homozyg-snp <min var count> –homozyg-kb <min length> –homozyg-density <max inverse density (kb/var)> –homozyg-gap <max internal gap…

Continue Reading Runs of homozygosity in Plink

Identifying RNA-seq reads containing polyA stretch

I’m in the need to filter our RNA-seq data for reads that contain a polyA stretch (e.g. with more than 6 A’s). I need to recover those reads, not discard them. The data is paired end and stranded. So, when dealing with paired reads in 2 files they should always…

Continue Reading Identifying RNA-seq reads containing polyA stretch

bcftools mpileup before bcftools call

bcftools mpileup before bcftools call 1 I want to variant call using bcftools call. However, when researching, I see a lot of people running bcftools mpileup before doing the actual variant calling with call. For example (from here): bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf…

Continue Reading bcftools mpileup before bcftools call

Sr Staff Bioinformatics Scientist Emerging Solutions Jobs – JobsOffices

Job Brief We have a vacancy of Sr Staff Bioinformatics Scientist Emerging Solutions in our company, Illumina. This vacancy is based in Singapore Singapore. Please go through the job detail mentioned below. Position Title: Sr Staff Bioinformatics Scientist Emerging Solutions Company: Illumina Work Type: Full Time City of work: Singapore…

Continue Reading Sr Staff Bioinformatics Scientist Emerging Solutions Jobs – JobsOffices

RNA-Seq. Isoform expression data.

RNA-Seq. Isoform expression data. 0 I have been given a list of DE genes with multiple isoforms of the same gene after performing RNA-seq. The problem is that they have the same gene name and are identified by the same name during the pathway analysis, and most of them have…

Continue Reading RNA-Seq. Isoform expression data.

Change names of all sequences in a MSA

Change names of all sequences in a MSA 1 I have a multiple sequence alignment where the names for each sequences are as follows >gi|AF266048.1|taxonid|126164|organism|Macromia splendens|seqid|AF266048.1|description|Macromia splendens small subunit ribosomal RNA gene partial sequence; mitochondrial gene for mitochondrial product What I’d like is to have >Macromia_splendens. I’m not sure how…

Continue Reading Change names of all sequences in a MSA

Guiding on a small bioinformatics research project start from project design – Freelance Job in Project Management – Less than 30 hrs/week – undefined

I am working on CRISPR-Cas9 endonuclease and need to finish a small bioinformatics study related to it. I need consultation on project design. The project need to be finish within a year and dry lab work only. The outcome of the project must be positive results…(I know it sounds undue…)…

Continue Reading Guiding on a small bioinformatics research project start from project design – Freelance Job in Project Management – Less than 30 hrs/week – undefined

I had more Gmod pics to post but Steam is acting fucky right now so some of them didn’t upload and I can’t email them to myself because hotel wifi is shit

memepedia log in add meme Animals & Nature Anime & Manga Art & Creative Cars Celebrities Gaming Girls Internet Memes Movies Other Politics Science & Tech Sports TV shows log in new featured top memes memes catalog Animals & Nature Anime & Manga Art & Creative Cars Celebrities Gaming Girls…

Continue Reading I had more Gmod pics to post but Steam is acting fucky right now so some of them didn’t upload and I can’t email them to myself because hotel wifi is shit

How do I get description in BLAST?

How do I get description in BLAST? 0 Hi, all. I’m trying to get a description to the gene list using BLAST. I created the original database with the following command and did BLAST, but my output shows a lot of N/A. $ makeblastdb -in caenorhabditis_elegans.PRJNA13758.WBPS16.protein.fa -out elegansdb -dbtype prot…

Continue Reading How do I get description in BLAST?

UCD Bioinformatics Core Workshop

Prepare your environment for Monocle Create an RStudio project In the R console run the following commands to install the needed packages to run Monocle3 if (!any(rownames(installed.packages()) == “remotes”)){ if (!requireNamespace(“BiocManager”, quietly = TRUE)) install.packages(“BiocManager”) BiocManager::install(“remotes”) } library(remotes) if (!any(rownames(installed.packages()) == “Seurat”)){ BiocManager::install(“Seurat”) } library(Seurat) if (!any(rownames(installed.packages()) == “R.utils”)){ BiocManager::install(“R.utils”)…

Continue Reading UCD Bioinformatics Core Workshop

Bioconductor/EuroBioC2022: European Bioconductor conference website 2022

GitHub – Bioconductor/EuroBioC2022: European Bioconductor conference website 2022 Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time This repository contains material for the European Bioconductor annual conference. View the conference web site Make sure Hugo is installed. Check hugo version Clone the repository and…

Continue Reading Bioconductor/EuroBioC2022: European Bioconductor conference website 2022

Next-Generation Dna Sequencing Inf 2E Cb BOOKH NEW 9781621821236

Next-generation DNA sequencing (NGS) techlogy has revolutionized biomedical research, making geme and RNA sequencing an affordable and frequently used tool for a wide variety of research applications including variant (mutation) discovery, gene expression, transcription factor analysis, metagemics, and epigenetics. Bioinformatics methods to support DNA sequencing have become and remain a…

Continue Reading Next-Generation Dna Sequencing Inf 2E Cb BOOKH NEW 9781621821236

Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human

doi: 10.1159/000518930. Online ahead of print. Jian-Chun He  1 , Shao-Ying Li  1 , Wen-Zhi He  1 , Jia-Jia Xian  1 , Xiao-Yan Ma  1 , Yan-Chao Wang  1 , Min-Cong Zhang  1 , Guo-Xin Ye  1 , Bo Liang  2 , Qin Xia  3 , Qing Li  1 Affiliations Expand Affiliations 1 Key Laboratory for Major Obstetric Diseases of…

Continue Reading Application of Restriction Site-Associated DNA Sequencing (RAD-Seq) for Copy Number Variation and Triploidy Detection in Human

Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how?

Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how? 0 Hi, I am re-analysing a publicly available single-cell RNA-seq dataset with two samples (plus minus treatment) and have downloaded preprocessed data from the geodataset as two .csv files. The authors state these files contain matrices that have…

Continue Reading Twice as many nFeature_RNA than nCount_RNA = more cell complexity? but how?

In Seurat, How Do nCount_RNA Differ from nFeature_RNA?

In Seurat, How Do nCount_RNA Differ from nFeature_RNA? 2 I’m reading up on the Seurat user guide: satijalab.org/seurat/v3.1/pbmc3k_tutorial.html And they mention for QC utilizing The number of unique genes detected in each cell and The total number of molecules detected within a cell They then refer to them as nCount_RNA…

Continue Reading In Seurat, How Do nCount_RNA Differ from nFeature_RNA?

Postdoctoral Fellow – Computational Analysis of Microbiome Data

We are seeking a highly motivated computational biologist to join the research group of Peer Bork within the Structural and Computational Biology Unit as a postdoctoral fellow. This bioinformatics group works on a wide range of topics with a current focus on microbiome analysis in ecosystems like the human gut…

Continue Reading Postdoctoral Fellow – Computational Analysis of Microbiome Data

GENOMICS LIBRARY PREPARATIONS, DNA/RNA EXTRACTION, DNA METHYLATION SEQUENCING, RNA-SEQUENCING AND MASS SPECTROMETRY FOR RESEARCH SERVICES.

From: Federal Procurement Data System(Federal) Start Date 01 Sep, 2021 (1 month ago) Due Date 31 Aug, 2026 (in about 4 years) Opportunity Type Contract Opportunity Identifier 36C24121D0019 Customer / Agency VETERANS AFFAIRS, DEPARTMENT OF Location USA, GENOMICS LIBRARY PREPARATIONS, DNA/RNA EXTRACTION, DNA METHYLATION SEQUENCING, RNA-SEQUENCING AND MASS SPECTROMETRY FOR…

Continue Reading GENOMICS LIBRARY PREPARATIONS, DNA/RNA EXTRACTION, DNA METHYLATION SEQUENCING, RNA-SEQUENCING AND MASS SPECTROMETRY FOR RESEARCH SERVICES.

The Biostar Handbook. A bioinformatics e-book for beginners.

March, 2020: Coronavirus Genome Analysis A new book has been released in the Biostar Handbook series: The book introduces readers to the practical aspects of investigating data from a viral outbreak. January, 2020: RNA-Seq by Example A new book has been released in the Biostar Handbook series: A step by…

Continue Reading The Biostar Handbook. A bioinformatics e-book for beginners.

KEGG ENZYME: 1.7.2.7

Entry EC 1.7.2.7                  Enzyme                                  Name Class Oxidoreductases;Acting on other nitrogenous compounds as donors;With a cytochrome as acceptorBRITE hierarchy Sysname hydrazine:ferricytochrome-c oxidoreductase Reaction(IUBMB) hydrazine + H2O + 3 ferricytochrome c = nitric oxide + ammonium + 3 ferrocytochrome c [RN:R09799] Reaction(KEGG) Substrate Product nitric oxide [CPD:C00533]; ammonium; ferrocytochrome c [CPD:C00126] Comment The enzyme,…

Continue Reading KEGG ENZYME: 1.7.2.7

Sample ID ERROR in converting dosage file (.txt) to VCF in PLINK 2.0

Sample ID ERROR in converting dosage file (.txt) to VCF in PLINK 2.0 0 Hi, I have a dosage file (.txt format; alternative allele count 0-2) that I would like to convert to a VCF through PLINK 2.0 but am running into sample ID issues. I am attempting the following…

Continue Reading Sample ID ERROR in converting dosage file (.txt) to VCF in PLINK 2.0

Do we need to filter out the 0 counts sgRNA in CRISPR analysis?

Do we need to filter out the 0 counts sgRNA in CRISPR analysis? 0 Hi, I’m doing CRISPR analysis and there is a question, when we perform CRISPR analysis, is there a step to remove low count sgRNAs from control and/or treatment samples? The reason of this question is that,…

Continue Reading Do we need to filter out the 0 counts sgRNA in CRISPR analysis?

New EXIMIA MAGNIFICA – FREEZ UP Ultrasound Electroporation Cryo Cosmetic General Um zu verkaufen

Few applications, zero recovery times, extraordinary results For the face : Evident anti-aging action Increase metabolic reactions Improve the quality of the skin Stimulate the microcirculation and increase capillary permeability Re-oxygenate and recompact the tissues Firm and reshape the face Magnifica is an innovative and exclusive mix of «Technology +…

Continue Reading New EXIMIA MAGNIFICA – FREEZ UP Ultrasound Electroporation Cryo Cosmetic General Um zu verkaufen

using modeltest-ng on an RNA virus

using modeltest-ng on an RNA virus 0 I wish to use modeltest-ng on a RNA virus. The genome sequences I have are cDNA sequences. When I enter them into modeltest-ng do I say they are DNA which they are, or RNA from which they were derived? Or do I need…

Continue Reading using modeltest-ng on an RNA virus

How do I upload my Ancestry raw dna?

Hello Tyrone, Thank you for indicating in WikiTree that you have tested with AncestryDNA.  Please register at ‪GEDmatch.com‬ and follow GEDmatch’s instructions to upload your AncestryDNA results there.  Or see step by step instructions at www.irelanddavis.com/dna/gedmatch/default.aspx.  This video also shows how: www.youtube.com/watch?v=-jpgxyqTLlk Uploading to GEDmatch will allow you to find matches with relatives who…

Continue Reading How do I upload my Ancestry raw dna?

H20 AutoML : kaggle

Search within r/kaggle Read more here: Source link

Continue Reading H20 AutoML : kaggle

Why do we log transform and scale data prior to PCA for scRNA-seq analysis

Why do we log transform and scale data prior to PCA for scRNA-seq analysis 0 Hi, I have a query as to why it is necessary to both log transform, and center and scale, scRNA-seq data prior to performing PCA. I thought the purpose of both of these steps was…

Continue Reading Why do we log transform and scale data prior to PCA for scRNA-seq analysis

Bullsquid game : gmod

Search within r/gmod r/gmod Read more here: Source link

Continue Reading Bullsquid game : gmod

Estimating the level of cytokine and chemokine from BulkRNAseq count matrix

Estimating the level of cytokine and chemokine from BulkRNAseq count matrix 0 Dear Seniors/members, Hope you’re doing great. I believe there are members of Biostar doing some immuno-oncology projects through RNA Sequencing. Cytokines/chemokines are the protein secreted by immune cells that serve as languages for immune cells to talk to…

Continue Reading Estimating the level of cytokine and chemokine from BulkRNAseq count matrix

Rise in Technological Advancements in DNA Sequencing Drive the Growth

DNA Sequencing Market Sequencing by synthesis (SBS), is one of the most influential and greatly adopted DNA sequencing technologies used by researchers and scientists globally” — Allied Market Research PORTLAND, OR, UNITED STATES, October 17, 2021 /EINPresswire.com/ — “DNA Sequencing Market by Product, Application, Technology, and End User: Global Opportunity…

Continue Reading Rise in Technological Advancements in DNA Sequencing Drive the Growth

EDGE-pro paired end read input

Hi, I am running EDGE-pro for prokaryotic RNA seq analysis for differential gene expression. ccb.jhu.edu/software/EDGE-pro/ I have paired end read data. The manual states ( ccb.jhu.edu/software/EDGE-pro/MANUAL ) // *MANDATORY FILES: -g genome: fasta file containing bacterial genome. If multiple chromosomes/plasmids exist, they must be combined into one file before running…

Continue Reading EDGE-pro paired end read input

Analysis of .ab1 file from sanger sequencer in galaxy

Analysis of .ab1 file from sanger sequencer in galaxy 0 Hi.. has anyone worked with .ab1 files in the galaxy? I know the workflow of RNAseq analysis but currently, I have .ab1 files(forward and reverse) from the sanger sequencer, so I need to work on that. Any clue will be…

Continue Reading Analysis of .ab1 file from sanger sequencer in galaxy

Differential expression analysis (DEA) of lncRNA

Differential expression analysis (DEA) of lncRNA 0 Hi all, I’m relatively new to RNA-seq analysis and want to perform differential expression analysis (DEA) of lncRNAs. I have read multiple different protocols and I think the following method would be valid and I hoped to receive feedback on it: Would this…

Continue Reading Differential expression analysis (DEA) of lncRNA

Consensus on poly-a selected lncRNAs for differential expression analysis

Consensus on poly-a selected lncRNAs for differential expression analysis 0 Hi all, This is somewhat related to my previous question: I was wondering if there is a general consensus on the validity of poly-a selected lncRNAs for DEA. Would this have scientific value? Or would it always be better to…

Continue Reading Consensus on poly-a selected lncRNAs for differential expression analysis

Identification of electroporation sites in the complex lipid organization of the plasma membrane

Abstract The plasma membrane of a biological cell is a complex assembly of lipids and membrane proteins, which tightly regulate transmembrane transport. When a cell is exposed to a strong electric field, the membrane integrity becomes transiently disrupted by formation of transmembrane pores. This phenomenon, termed electroporation, is already utilized…

Continue Reading Identification of electroporation sites in the complex lipid organization of the plasma membrane

Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods

Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods Authors Park, KS[Park, Kyung Sun]; Ki, CS[Ki, Chang-Seok]; Kang, CI[Kang, Cheol-In]; Kim, YJ[Kim, Yae-Jean]; Chung, DR[Chung, Doo Ryeon]; Peck, KR[Peck, Kyong Ran]; Song, JH[Song, Jae-Hoon]; Lee, NY[Lee, Nam Yong] Issue Date May-2012 Publisher…

Continue Reading Evaluation of the GenBank, EzTaxon, and BIBI Services for Molecular Identification of Clinical Blood Culture Isolates That Were Unidentifiable or Misidentified by Conventional Methods

The value of updating GenBank accessions for supermatrix phylogeny: the case of the New Guinean marsupial carnivore genus Myoictis

Available online 16 October 2021, 107328 doi.org/10.1016/j.ympev.2021.107328Get rights and content Highlights • Taxonomic misattribution of GenBank accessions misleads Myoictis phylogeny. • A few misattributed accessions disproportionately mislead supermatrix phylogeny. • Updating these accessions corrects Myoictis supermatix phylogeny. • Myoictis melas is sister to all other Myoictis species. • We propose…

Continue Reading The value of updating GenBank accessions for supermatrix phylogeny: the case of the New Guinean marsupial carnivore genus Myoictis

KEGG ENZYME: 1.1.3.39

KEGG ENZYME: 1.1.3.39     ENZYME: 1.1.3.39 Help Entry EC 1.1.3.39                 Enzyme                                  Name nucleoside oxidase (H2O2-forming) Class Oxidoreductases;Acting on the CH-OH group of donors;With oxygen as acceptorBRITE hierarchy Sysname nucleoside:oxygen 5′-oxidoreductase (H2O2-forming) Reaction(IUBMB) adenosine + 2 O2 + H2O = 9-riburonosyladenine + 2 H2O2 (overall reaction) [RN:R05695]; (1a) adenosine + O2 = 5′-dehydroadenosine…

Continue Reading KEGG ENZYME: 1.1.3.39

KEGG ENZYME: 2.1.4.1

Entry EC 2.1.4.1                  Enzyme                                  Name glycine amidinotransferase;arginine-glycine amidinotransferase;arginine-glycine transamidinase;glycine transamidinase Class Transferases;Transferring one-carbon groups;AmidinotransferasesBRITE hierarchy Sysname L-arginine:glycine amidinotransferase Reaction(IUBMB) L-arginine + glycine = L-ornithine + guanidinoacetate [RN:R00565] Reaction(KEGG) Substrate Product Comment Canavanine can act instead of arginine. History EC 2.1.4.1 created 1961 as EC 2.6.2.1, transferred 1965 to EC 2.1.4.1 Pathway ec00260  …

Continue Reading KEGG ENZYME: 2.1.4.1

gmod post processing not working

In principle it is working. on gmod possessor mod. Found inside – Page 241The problem is that a postprocessing vertex for argument y in the call to Add from A is included in A’s procedure … summary information consists of the following sets , which are computed for each procedure…

Continue Reading gmod post processing not working

gmod roleplay model pack

Update: Fixed bumpmaps and rigging errors for all! –I did not make this addon, I’m only supporting the community by adding it to the Gmod 13 workshop.–. Go the the GMOD Textures Page. However, I feel that this pack has both more content at a higher quality than pack 1,…

Continue Reading gmod roleplay model pack

Project Research Scientist II Jobs in Belgaum at ICMR NITM

– Advertisement – Project Research Scientist II Jobs in Belgaum at ICMR NITM – Apply Now Project Research Scientist II Jobs in Belgaum: On 16.10.2021, ICMR NITM announced job notification for the post of Project Research Scientist II had been released officially. M.Sc, M.Phil/Ph.D pass Can apply for this job…

Continue Reading Project Research Scientist II Jobs in Belgaum at ICMR NITM

Technical Support Specialist – BioInformatics at Invitae

POSITION SUMMARYThe Technical Support Specialist provides first level technical support on Invitae Somatic Oncology products from the Invitae office in Boulder, CO. This individual will escalate customer inquiries effectively, collect customer feedback and share this with internal teams to improve products. This individual will assist in coordinating activities for special…

Continue Reading Technical Support Specialist – BioInformatics at Invitae

how to interpret very short effective length in Salmon output

how to interpret very short effective length in Salmon output 0 Hello I am interested in a specific transcript in the quant.sf output file of Salmon. This transcript has length of 153 nt and, according to salmon, an effective length of 13-15 nt, depending on the sample. The transcript have…

Continue Reading how to interpret very short effective length in Salmon output

What is bigwig file?

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

Continue Reading What is bigwig file?

eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer’s disease mouse model

eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer’s disease mouse model 2 Hi I am a beginner to prepare eQTL analysis using mouse model for alzheimer’s disease. Is it possible to conduct eQTL analysis using ONLY brain RNA-seq data derived from 5XFAD or 3xtg mouse (The Jackson…

Continue Reading eQTL analysis method (or pipeline) using ONLY RNA-seq data of alzheimer’s disease mouse model

In Utero Electroporation ~ 35+ images supplement to molecular and morphological heterogeneity of, in utero electroporation with green, a schematic illustration showing in utero

This post is called In Utero Electroporation. You can download all the image about In Utero Electroporation free of charge. Here are the image gallery of In Utero Electroporation, if you want the image or such as this post please add with us to share this post to your public…

Continue Reading In Utero Electroporation ~ 35+ images supplement to molecular and morphological heterogeneity of, in utero electroporation with green, a schematic illustration showing in utero

teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol

GitHub – teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol Files Permalink Failed to load latest commit information. Type Name Latest commit message Commit time BACKGROUND…

Continue Reading teomotun/LAMMPS-Water-Methanol-Simulation: Molecular Dynamics Simulation of Water-Methanol Mixture to determine physical properties like self-diffusion coefficient, density and shear viscosity for a system consisting of 216 molecules of water and 216 molecules of methanol

Download all cases from TCGAbiolinks

Hi all, I would like to download the bulk RNA-seq data for all patients in the TCGA-LUAD cohort using TCGAbiolinks. Does this exist as a single matrix? I have read the package vignette and can download individual cases however does TCGAbiolinks facilitate downloading a single matrix of all the patients?…

Continue Reading Download all cases from TCGAbiolinks

Nose hoover lammps manual

Nose hoover lammps manual 科学网—[转载]谈谈分子模拟中的能量最小化,弛豫和平衡态 – 周龙 …NVT run with LAMMPS | Tools and tricks for computational A serious man with a comic face-walrus mustache, had long ago wanted to tear the old girl down and replace her with a gleaming…

Continue Reading Nose hoover lammps manual

What files (fasta, GTF) do I need for RNA seq analysis

What files (fasta, GTF) do I need for RNA seq analysis 1 I am very new to programming in general, and I’m trying my best to teach myself R for analyzing RNA-seq data we have. I am using this guide and have gotten to the step where I need to…

Continue Reading What files (fasta, GTF) do I need for RNA seq analysis

correlation analysis

correlation analysis 0 Hello everyone, I have two datasets. One is normalised_counts.txt which is the results of deseq2 analysis and the other is a predixcan file which have counts for each gene for all the chromosomes. I have to do Pearson correlation to figure out how many genes in our…

Continue Reading correlation analysis

Development Scientist – Bioinformatics job with New England Biolabs

New England Biolabs (NEB) is seeking a computational scientist to work collaboratively with bench scientists. We will collaboratively construct software methods, analyze sequence results, and integrate data from instrumentation, ultimately creating high quality, rigorously tested, and provably excellent products. NEB provides an ideal working environment including high quality computational infrastructure,…

Continue Reading Development Scientist – Bioinformatics job with New England Biolabs

Job Clinical Data Manager Role At Unicon Pharma, Massachusetts

– Advertisement – Job Clinical Data Manager Role At Unicon Pharma, Massachusetts – Apply Now About the job The CDML is accountable for all Data Management aspects of the assigned compound and indication from initiation till the closure of activities, ensuring that clinical data completeness, accuracy, and consistency meet the…

Continue Reading Job Clinical Data Manager Role At Unicon Pharma, Massachusetts

What is eggnog better than previous annotation in terms of?

What is eggnog better than previous annotation in terms of? 0 Hi, all. I used eggnog to get annotations in de novo RNAseq analysis But I haven’t understand the merit. What is eggnog better than previous annotation(ex. BLAST etc.) in terms of? Although I had read ths instruction in eggnog,…

Continue Reading What is eggnog better than previous annotation in terms of?

nja Eagle City (gmod) by rocketboy3005 on DeviantArt

Link to map:steamcommunity.com/sharedfiles… Another map from Ninjala finally ported over to Gmod. This time, it is Eagle City. Since Eagle City has a Night version, thanks to Story’s boss map. We can have the far and sky models to be night instead of day. I still consider these maps I…

Continue Reading nja Eagle City (gmod) by rocketboy3005 on DeviantArt

Running ATAC-Seq pipeline from ENCODE

Running ATAC-Seq pipeline from ENCODE 1 SLURM is simply a scheduler on HPC systems. You can (probably) just save the script and run it as bash that_script.sh. Alternatively, consider the nf-core ATAC-seq pipeline: nf-co.re/atacseq Login before adding your answer. Traffic: 1212 users visited in the last hour Read more here:…

Continue Reading Running ATAC-Seq pipeline from ENCODE

rreformat.sh and stats.sh program in BBmap

rreformat.sh and stats.sh program in BBmap 1 Hello there, i am working with RNA seq data and have paired end reads. While running the reformat.sh command I am getting this out put: Set INTERLEAVED to false Exception in thread “main” java.lang.AssertionError: File 19213R-08-01_S16_L002_R1_001.fastq exists and overwrite=false what does it mean?…

Continue Reading rreformat.sh and stats.sh program in BBmap

Risk of developing a mitochondrial DNA deletion disorder.

Authors Chinnery, PF, DiMauro, S, Shanske, S, Schon, EA, Zeviani, M, Mariotti, C, Carrara, F, Lombes, A, Laforet, P, Ogier, H, Jaksch, M, Lochmüller, H, Horvath, R, Deschauer, M, Thorburn, DR, Bindoff, LA, Poulton, J, Taylor, RW, Matthews, JNS, Turnbull, DM Abstract BACKGROUND: Pathogenic mitochondrial DNA (mtDNA) mutations are found…

Continue Reading Risk of developing a mitochondrial DNA deletion disorder.