Category: R

Annotation of differentially methylated region or based in methylkit using genomation, how to find annotation file?

Annotation of differentially methylated region or based in methylkit using genomation, how to find annotation file? 0 Hi. I am performing differential methylation analysis in grapevine (vitis vinifera). To annotate differentially methylated region or bases i need the annotation file i.e., bed file. From where should i find that annotation…

Continue Reading Annotation of differentially methylated region or based in methylkit using genomation, how to find annotation file?

PhD Candidate Maastricht University | ‘Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles’

Ph.D. Candidate, Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles in the Department of Bioinformatics, School NUTRIM at the Faculty of Health, Medicine and Life Sciences Deadline: 14 November 2021 More information and apply at Academic Transfer: AT2021.283 Specifications 36—40 hours per week €2434—€3111 per month…

Continue Reading PhD Candidate Maastricht University | ‘Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles’

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

Aligning One Protein Sequence With A Multiple Sequence Alignment

Aligning One Protein Sequence With A Multiple Sequence Alignment 5 Given one protein sequence and a multiple sequence alignment(MSA) of a set of proteins, I want to align the protein sequence with that MSA with out changing the MSA. Do you know any tool that is cable of doing this?…

Continue Reading Aligning One Protein Sequence With A Multiple Sequence Alignment

Anyone could help me with cutadapt?

I’, trying to trim my primers off from Illumina sequences. I ‘ve amplified with: Diat_rbcL_F1 AGGTGAAGTAAAAGGTTCWTACTTAAA, Diat_rbcL_F2 AGGTGAAGTTAAAGGTTCWTAYTTAAA and Diat_rbcL_F3 AGGTGAAACTAAAGGTTCWTACTTAAA as Forward primers and Diat_rbcL_R1 5’CCTTCTAATTTACCWACWACTG 3’ (Reverse Complement: 3’CAGTWGTWGGTAAATTAGAAGG 5’) and Diat_rbcL_R2 5’CCTTCTAATTTACCWACAACAG 3’ (Reverse Complement: 3’CTGTTGTWGGTAAATTAGAAGG 5’) Reverse primers. First, I used PEAR to assembly paired reads…

Continue Reading Anyone could help me with cutadapt?

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”

no restriction enzyme in process_radtags

no restriction enzyme in process_radtags 0 Hello: I have a problem using process_radtags(stack v2.55). My restriction enzyme is taqaI, but there is only taqI in the program. Are these two the same? Thanks! process_radtags restriction stacks enzyme • 15 views Login before adding your answer. Read more here: Source link

Continue Reading no restriction enzyme in process_radtags

Mouse RefCDS for dNdScv package

Mouse RefCDS for dNdScv package 0 Hi all I am trying to run the dNdScv package to identify mutations that are under positive selection. The dataset I am working with is sequencing data from mouse tumours using a targeted gene panel. The default for the package is using human data….

Continue Reading Mouse RefCDS for dNdScv package

Methylation coordinates for hg19

Methylation coordinates for hg19 1 Hi, Are there any resources to grab the coordinates of the genome with known methylation sites and coordinates, be it tissue specific or more general methylation landscape? If there are any databases I can extract this information from I would be very happy to know….

Continue Reading Methylation coordinates for hg19

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

EBI European Nucleotide Archive (ERA) aspera access broken

EBI European Nucleotide Archive (ERA) aspera access broken 0 I’m trying to download FASTQ files from the ENA via aspera. FTP still works. ascp -QT -P33001 -l 200m -i /home/me/.aspera/connect/etc/asperaweb_id_dsa.openssh era-fasp@fasp.sra.ebi.ac.uk:/vol1/fastq/SRR663/009/SRR6639099/SRR6639099_1.fastq.gz ./ As of sometime last week I am constantly getting: Session Stop (Error: failed to authenticate) ascp: failed to…

Continue Reading EBI European Nucleotide Archive (ERA) aspera access broken

What does it “mean” when MrBayes chooses rtREV as substitution model?

What does it “mean” when MrBayes chooses rtREV as substitution model? 0 I am doing phylogenetic analysis of a highly conserved protein’s AA sequences over a wide range of Eukaryote taxa using MrBayes’ mcmc method. MrBayes, when run in mixed mode, consistently chooses the rtREV model, while ML methods (prottest3…

Continue Reading What does it “mean” when MrBayes chooses rtREV as substitution model?

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

the way to find pseudogenes in my scaffolds of genome

the way to find pseudogenes in my scaffolds of genome 3 Hello Recently, I assembled genome of a beetle living underground. My interest is searching pseudogenes (premature stop codon or frameshifts). I conducted tblastn using a few genes of model organisms (Tribolium) as query. But no premature stop codons were…

Continue Reading the way to find pseudogenes in my scaffolds of genome

biomaRt does not convert entrez gene id to ensembl gene id

biomaRt does not convert entrez gene id to ensembl gene id 0 I am trying to convert my entrez gene_id to ensembl gene_id. Here is my R codes > library(biomaRt) > ensembl<- useEnsemblGenomes(biomart = “plants_mart”) > searchDatasets(ensembl,pattern = “Beta”) dataset description 14 bvulgaris_eg_gene Beta vulgaris genes (RefBeet-1.2.2) version 14 RefBeet-1.2.2…

Continue Reading biomaRt does not convert entrez gene id to ensembl gene id

Sort a sub column within a column while keeping the feature (LINUX)

I have a vcf file with these column headers: #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BS_25YES2E3 BS_G5B6AD28 BS_QCGPE1ZX A sample feature within that vcf file chr1 10450 . T C 27.94 VQSRTrancheSNP99.90to100.00+ AC=1;AF=0.167;AN=6;BaseQRankSum=-1.676e+00;ClippingRankSum=0.789;DP=102;ExcessHet=4.7712;FS=4.868;MLEAC=1;MLEAF=0.167;MQ=34.67;MQRankSum=-1.084e+00;PG=0,0,0;QD=1.55;ReadPosRankSum=-2.169e+00;SOR=0.707;VQSLOD=-1.050e+01;culprit=MQ;ANN=C|upstream_gene_variant|MODIFIER|**DDX11L1**|ENSG00000223972|Transcript|ENST00000450305|transcribed_unprocessed_pseudogene|||||||||||1560|1||SNV|HGNC|HGNC:37102||||chr1:g.10450T>C,C|upstream_gene_variant|MODIFIER|DDX11L1|ENSG00000223972|Transcript|ENST00000456328|processed_transcript|||||||||||1419|1||SNV|HGNC|HGNC:37102|YES|||chr1:g.10450T>C,C|downstream_gene_variant|MODIFIER|WASH7P|ENSG00000227232|Transcript|ENST00000488147|unprocessed_pseudogene|||||||||||3954|-1||SNV|HGNC|HGNC:38034|YES|||chr1:g.10450T>C GT:AD:DP:FT:GQ:JL:JP:PL:PP 0/0:28,0:28:lowGQ:0:1:1:0,0,663:0,0,666 0/1:13,5:18:PASS:35:1:1:34,0,342:35,0,345 0/0:44,0:44:lowGQ:0:1:1:0,0,802:0,0,805 The portion in bold is what I want (DDX11L1). I…

Continue Reading Sort a sub column within a column while keeping the feature (LINUX)

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

Bioinformatics Academia jobs in Medford

Broaden your search Refine your search To see more jobs like this, please sign up for Job Alerts Found 1 job Postdocs, PhD students, Master/PhD students and Research Assistants Top job …

Continue Reading Bioinformatics Academia jobs in Medford

About Foreign Fields in VCF (4.3)

About Foreign Fields in VCF (4.3) 0 I was looking at the VCF format 4.3 here – page 7 and 4.2 page 4. More or less they are similar, stating 8 mandatory and fixed, tab delimited columns. I was bit lost about the term ‘fixed’, I am wondering, say for…

Continue Reading About Foreign Fields in VCF (4.3)

Counting the number of SNPs (VCF) for each genomic coordinates (BED)

Counting the number of SNPs (VCF) for each genomic coordinates (BED) 1 I want to count the number of recorded variations for each genomic coordinates of a .bed file from the corresponding .vcf file. I guess it should be solved by vcftools, but I could not find any suitable option…

Continue Reading Counting the number of SNPs (VCF) for each genomic coordinates (BED)

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

KOBAS on Galaxy local

KOBAS on Galaxy local 0 Hello, I’m trying to setting up Galaxy on my PC. I need to use the tool “KOBAS annotate” & “KOBAS identify”. I would need help in setting up the field “BLAST protein database” since I don’t understand how to configure it. I tried to download…

Continue Reading KOBAS on Galaxy local

Postdoctoral Fellowship in Genetic epidemiology and Bioinformatics in Boston, MA for Brigham and Women’s Hospital, Harvard Medical School

Use this area to filter your search results. Each filter option allows for multiple selections. DisciplineAcademic / Research (105)Academic/Faculty (985)Admin / Clerical (3)Advanced Practice Registered Nurses / Physician Assistants (1)Agricultural Engineering (1)Allied Health (115)Attorney (3)Biology (8)Biomedical Engineering (15)Computer and Information Science (1)Engineering (0)Executive (21)General Nursing (7)Industrial Engineering (1)Mental Health/Social Services…

Continue Reading Postdoctoral Fellowship in Genetic epidemiology and Bioinformatics in Boston, MA for Brigham and Women’s Hospital, Harvard Medical School

How to include a Jmol Console Script in a Python Script

How to include a Jmol Console Script in a Python Script 0 I have created a python script and a Jmol Console Script. How can I load the Jmol Console Script into the Python Script? For example I have this Jmol Console Script: load ‘ligand_PDB_entry_prompt’ select water ; delete selected…

Continue Reading How to include a Jmol Console Script in a Python Script

autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

Source: ncbi-acc-download Version: 0.2.7-1 Severity: important Tags: ftbfs Dear Maintainer, I am trying to assess the side effects of an upgrade of the package python-biopython to 1.79 to its reverse dependencies. Pseudo-excuses look alright, except for ncbi-acc-download [1]. [1]: release.debian.org/britney/pseudo-excuses-experimental.html [2]: ci.debian.net/data/autopkgtest/unstable/amd64/n/ncbi-acc-download/15982166/log.gz The full log [2] shows variations around the…

Continue Reading autopkgtest failure with python-biopython 1.79+dfsg-1~0exp0 in experimental

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?

Where can I find a complete mapping of Gencode versions to Ensembl versions?

Where can I find a complete mapping of Gencode versions to Ensembl versions? 2 The UCSC track browser has a page listing all the Gencode tracks currently available along with their corresponding Ensembl versions. For example, the latest version at time of writing says “All GENCODE annotations from V37 (Ensembl…

Continue Reading Where can I find a complete mapping of Gencode versions to Ensembl versions?

Stacks process_radtags question and scripts

Stacks process_radtags question and scripts 1 How I can modify the quality score to retain more reads in stacks process_radtags? I have paired-end reads from Illumina Next Seq 500. This is my script: process_radtags -1 MAGICR1_T.fastq.gz -2 MAGICR2_T.fastq.gz -b Barcode2.txt -o /home/mdominguez/demult_MAGIC_b –renz_1 sphI –renz_2 sau3AI -E phred33 –barcode_dist_2 3…

Continue Reading Stacks process_radtags question and scripts

how to set process_radtags program barcode informations

how to set process_radtags program barcode informations 0 Hello,recently, I have been using Stacks for GBS data , but I encountered a problem. When using process_radtags program of Stacks , barcode information is required by default, but my original data is clean_data, and the company told me that barcode information…

Continue Reading how to set process_radtags program barcode informations

how to map Pacbio CCS fastq

how to map Pacbio CCS fastq 1 I have a Pacbio CCS fastq like this I want to map to genome, and this is my command and out. I want to know how to solve it. Is this fastq correct? Thanks minimap2 Pacbio • 25 views It might pay to…

Continue Reading how to map Pacbio CCS fastq

Empty output from UMItools dedup after fastp processing

Empty output from UMItools dedup after fastp processing 0 Hello, I have been running into an interesting error during my sequencing analysis.We have a paired-end library with UMIs on both ends of the fragments, 6 nts each, for a total of 12 nt.Now, I have been using fastp for preprocessing…

Continue Reading Empty output from UMItools dedup after fastp processing

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

RRHO2 Heatmaps uneven size

RRHO2 Heatmaps uneven size 0 Hi. I’ve used the RRHO2 package to compare gene expression between two groups carried out in two separate studies. On the left is Treatment 1 vs Control for two studies and on the right is Treatment 2 vs Control for the same two studies. I…

Continue Reading RRHO2 Heatmaps uneven size

when choosing the best K for ADMIXTURE should I use delta K method or cross validation error

when choosing the best K for ADMIXTURE should I use delta K method or cross validation error 0 I ran ADMIXTURE with my VCF data The ADMIXTURE manual says that I can find the appropriate K by checking the cross validation error. what I read about cross validation error is…

Continue Reading when choosing the best K for ADMIXTURE should I use delta K method or cross validation error

Problem aligning ggtree circular tree labels to right angles

Problem aligning ggtree circular tree labels to right angles 0 Hi, I have made a very nice tree using ggtree package. It is circular but with the fan option – ie it has an open angle. The tree has different clades that I’ve highlighted and I also added a remark…

Continue Reading Problem aligning ggtree circular tree labels to right angles

Vtg 1940’s Baby Blanket Blue & White Cotton Circus Animals Elephant Dogs Bears

Model: unq848 Availability :  In Stock Vtg 1940’s Baby Blanket Blue & White Cotton Circus Animals Elephant Dogs Bears Model: unq848 Availability :  In Stock Notice: This product is available for flash sale,and stock is limited. In case of payment failure, please check the information carefully and confirm it again.If…

Continue Reading Vtg 1940’s Baby Blanket Blue & White Cotton Circus Animals Elephant Dogs Bears

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

How we can put PASS filters on all variants in your VCF file and create a separate file?

By default, we trust PASS filters on VCF files. If a VCF is not filtered or PASS filters are not present, we use a very basic universal filter that relies on QUAL (Quality) and DP (Depth), which is better than nothing. If you want to run all of your data…

Continue Reading How we can put PASS filters on all variants in your VCF file and create a separate file?

[lammps-users] compute bin/cylinder with a moving COM – #2 by akohlmey – LAMMPS Mailing List Mirror

You are confusing how LAMMPS input works. Fact is that c_COM[1] is a string not a number. To have a command recognize such a string as a reference to a compute instance global vector element and retrieve the value from it has to be programmed into the source code. If…

Continue Reading [lammps-users] compute bin/cylinder with a moving COM – #2 by akohlmey – LAMMPS Mailing List Mirror

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)

Senior Computational Scientist, Bioinformatics Job Champaign IL

Job Details Job Title: Senior Computational Scientist, Bioinformatics Location: Champaign, IL, Midwest United States, USA Company: Nutrien Ag Solutions, Inc Industry Sector: Agribusiness Industry Type: Chemical, Pesticide and Fertilizer Career Type: Job Type: Full Time Minimum Years Experience Required: N/A Salary: Competitive 0 “> …

Continue Reading Senior Computational Scientist, Bioinformatics Job Champaign IL

Importance of Multiple Sequence Alignment

Importance of Multiple Sequence Alignment 0 I am planning to work on designing “hardware accelerator for Multiple Sequence Alignment (MSA) tool, MAFFT”. I decided to select MAFFT algorithms as my research target because I found in publications that some of the MAFFT algorithms are more accurate compared to other solutions…

Continue Reading Importance of Multiple Sequence Alignment

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

Recommended mapper

Recommended mapper 0 I’m looking for a short read mapper to map metagenomics samples against wide range of microbial genomes. I just need to know the best mapping so aligner that optimized to find variants is unnecessary. I know that it is common to use Bowtie2 and BWA but wondering…

Continue Reading Recommended mapper

non-unique values when setting ‘row.names’ error in DESeq2

non-unique values when setting ‘row.names’ error in DESeq2 0 Hi Everyone! I am trying to run the DESeqDataSetFromMatrix() command using a specific dataset but I keep getting the following error. For some reason, R (version 4.0.5) is trying to assign the first column of my DataFrame to be the row…

Continue Reading non-unique values when setting ‘row.names’ error in DESeq2

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

Extracting named fasta sequences according to list with Biopython

Extracting named fasta sequences according to list with Biopython 0 Hi all, I’m trying to work out a quick script to extract a set of sequence fasta files from a multifasta and write them all to a new, single fasta file. To elaborate, I’ve got a proteome, and I want…

Continue Reading Extracting named fasta sequences according to list with Biopython

Diamond and Taxonomic information

Diamond and Taxonomic information 0 Hello, I successfully executed the diamond makedb and blastx processes, and obtained the data file containing also the taxonomic information. Of course, I ran the makedb in the correct way, including the needed files: diamond makedb -p 4 –in /storage/RefSeq/small.nonredundant_protein.faa –taxonmap /storage/RefSeq/prot.accession2taxid –taxonnames /storage/RefSeq/names .dmp…

Continue Reading Diamond and Taxonomic information

Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing

Author Correction: Generation of somatic mitochondrial DNA-replaced cells for mitochondrial dysfunction treatment “ρ(-)”. Consequently, Figure 2(g) legend has been modified accordingly,. “MirCs were generated from mitochondrial disease patient-derived (7S) fibroblasts. (a) mtDNA CN during the procedure of MirC generation. Fibroblasts that received gene transfer, designated as 7S_ρ(-) were cultivated with…

Continue Reading Precision modeling of mitochondrial disease in rats via DdCBE-mediated mtDNA editing

Haplotype and phylogenetic analyses suggest that one European-specific mtDNA background plays a role in the expression of Leber hereditary optic neuropathy by increasing the penetrance of the primary mutations 11778 and 14484.

Authors Torroni, A, Petrozzi, M, D’Urbano, L, Sellitto, D, Zeviani, M, Carrara, F, Carducci, C, Leuzzi, V, Carelli, V, Barboni, P, De Negri, A, Scozzari, R Abstract mtDNAs from 37 Italian subjects affected by Leber hereditary optic neuropathy (LHON) (28 were 11778 positive, 7 were 3460 positive, and 2 were…

Continue Reading Haplotype and phylogenetic analyses suggest that one European-specific mtDNA background plays a role in the expression of Leber hereditary optic neuropathy by increasing the penetrance of the primary mutations 11778 and 14484.

Print

%PDF-1.4 1 0 obj >endobj 2 0 obj >endobj 3 0 obj >/Parent 2 0 R /Resources >/ProcSet [/PDF /Text /ImageC /ImageI ]/XObject >/ExtGState >>>/MediaBox [0 0 595.3 841.9 ]/CropBox [0 0 595.3 841.9 ]/BleedBox [0 0 595.3 841.9 ]/Group >/Contents 4 0 R >>endobj 4 0…

Continue Reading Print

Bioconductor – ecolicdf

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see ecolicdf. ecolicdf Bioconductor version: 2.14 A package containing an environment representing the Ecoli.CDF file. Author: The Bioconductor Project Maintainer: Bioconductor Package Maintainer <maintainer at bioconductor.org> Citation (from within R, enter citation(“ecolicdf”)): Installation To…

Continue Reading Bioconductor – ecolicdf

Tools / Packages to assess allele specific methylation?

Tools / Packages to assess allele specific methylation? 0 Hi everyone, Are there any tools/packages/pipelines to assess allele specific methylation for human data? I have used the following methods: 1. TrimGalore > Bismark Alignment > SNPsplit (Read split)> Bismark (methylation call) or 2. TrimGalore > Bismark Alignment > Damefinder (Coverage/Meth…

Continue Reading Tools / Packages to assess allele specific methylation?

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

The National Institutes of Health hiring Bioinformatics – Novel High Throughput Sequencing Methods in Bethesda, Maryland, United States

Position DescriptionA computational biology position will be hired depending on the qualification and is available from October 2021. Research in bioinformatics focus on investigating high throughput sequencing data using novel methods. Work with available pipelines or develop new ones. Implementing various modeling and prediction techniques, including linear and nonlinear regression,…

Continue Reading The National Institutes of Health hiring Bioinformatics – Novel High Throughput Sequencing Methods in Bethesda, Maryland, United States

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

Blastx only uses one thread when word size is above 3

Blastx only uses one thread when word size is above 3 0 Hi all, I’m using blast version 2.12.0 and running the following command blastx -db my_db -query ecoli.fna -num_threads 8 -word_size 3 The query runs pretty fast and if I check the CPU usage is always around 600-700%. However,…

Continue Reading Blastx only uses one thread when word size is above 3

Code for Rstudio with TFBSTools package searching for trascription factors in fasta format DNA sequence

Code for Rstudio with TFBSTools package searching for trascription factors in fasta format DNA sequence 0 Hello, i want to make a code for RStudio in order to find what transcription factors found in my sequences. I have DNA sequences at FASTA format with 40 noucleotides. First i want to…

Continue Reading Code for Rstudio with TFBSTools package searching for trascription factors in fasta format DNA sequence

How to open 2 separate pymol windows from a script, and run commands after pymol window closes

How to open 2 separate pymol windows from a script, and run commands after pymol window closes 0 Hello, In short, I’m playing around with pymol and have come across 2 problems. How can I open 2 separate windows of pymol from the same script Closing pymol closes the entire…

Continue Reading How to open 2 separate pymol windows from a script, and run commands after pymol window closes

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?

Bioinformatics Analyst Resume Summary

PERL HTML NET PYTHON. Bioinformatics analyst resume summary. Fast Easy to Build Free Resumes. Looking for a challenging position as a bioinformatics analysts in an organization that provides an opportunity towards professional growth and development Summary of Knowledge Skills. Professional Summary Highly skilled bioinformatics analyst with strong research history and…

Continue Reading Bioinformatics Analyst Resume Summary

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)

Senior Computational Biologist I

Senior Computational Biologist I Company Overview At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence and improving outcomes. We’re treating cancer, one patient…

Continue Reading Senior Computational Biologist I

SR. Bioinformatics Software Engineer – CMO

Job:SR. Bioinformatics Software Engineer – CMO – MSKCC 0 Senior Bioinformatics Engineer Company Overview At Memorial Sloan Kettering (MSK), we’re not only changing the way we treat cancer, but also the way the world thinks about it. By working together and pushing forward with innovation and discovery, we’re driving excellence…

Continue Reading SR. Bioinformatics Software Engineer – CMO

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

Bioconductor – Developers’ Forum

The Bioconductor Developers’ Forum aims to provide a regular platform for Bioconductor developers to describe existing software infrastructure, to present plans for future developments, and discuss changes that may impact developers within the Bioconductor project. The goals we hope to address include: To inform other developers of ongoing or imminent…

Continue Reading Bioconductor – Developers’ Forum

Bioconductor – GGBase

    This package is for version 2.11 of Bioconductor; for the stable, up-to-date release version, see GGBase. GGBase infrastructure for genetics of gene expression package GGtools Bioconductor version: 2.11 infrastructure Author: VJ Carey <stvjc at channing.harvard.edu> Maintainer: VJ Carey <stvjc at channing.harvard.edu> Citation (from within R, enter citation(“GGBase”)): Installation…

Continue Reading Bioconductor – GGBase

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?

Illumina Read Stitching

Illumina Read Stitching 0 We have implemented the new software provided by Illumina in our mySeq. The application allows to turn off or on the parametre “Read Stitching”. From the Illumina website, I can understand what a stitched read is. However, I have run many samples with both parameters on…

Continue Reading Illumina Read Stitching

How best to handle multiple probes for single genes in survival analysis of Geo data

How best to handle multiple probes for single genes in survival analysis of Geo data 0 I imported some microarray data from Geo and was able to write a for loop that plots survival curves for high/low expression of each probe corresponding to a specific gene. Now I am interested…

Continue Reading How best to handle multiple probes for single genes in survival analysis of Geo data

IDR installation help

IDR installation help 0 I am seeking installation assistance. I have tried twice to install IDR. I first tried python 3 setup.py. install as instructed in the manual. I received the following error: [Errno 2] No such file or directory: ‘Library/Python/3.8/site-packages/test-easy-install-53208.write-test’ The installation directory you specified (via –install-dir, –prefix, or…

Continue Reading IDR installation help

Phosphorylation database

Phosphorylation database 0 Hi, I would like to ask if there is a phosphorylation database for human proteome which provides the information not only for the phosphorylation sites of a protein but also each targets. What I am looking for is phosphorylation interactions between proteins. Thanks in advance! phosphorylation database…

Continue Reading Phosphorylation database

High positive values in vcftools –het results

High positive values in vcftools –het results 0 Hello all, I am trying to find out the inbreeding coefficients of the individuals in my sample using vcftools –het filter. I am seeing very high positive values (as seen in the figure below). What does very high positive values mean? Is…

Continue Reading High positive values in vcftools –het results

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

FASTQ to VCF pipeline question

FASTQ to VCF pipeline question 0 Hello all, I am new with programming within bioinformatics and long story short, I’m practicing writing pipeline scripts starting with the fastq to VCF pipeline. I am basically at the point where I went from fastq to sorted-bam files, and as I went to…

Continue Reading FASTQ to VCF pipeline question

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

Freebayes for creating VCF : meaning of QUAL

Freebayes for creating VCF : meaning of QUAL 1 Hi, I have 10 sorted Bam files 5 Male and 5 Female. I used Freebayes to create vcf files separately and then merged all 10 together. (ploidy 8) The commands I used: freebayes -f $REF -p 8 $SORTED_BAM > $OUTPUT (for…

Continue Reading Freebayes for creating VCF : meaning of QUAL

Tech-i-s/techis-ds-kaggle-sentiment_analysis_movie_review_NLP: Kaggle Sentiment analysis of movie review using Natural Language Processing Project

Classify the sentiment of sentences from the Rotten Tomatoes dataset Go to Page… “There’s a thin line between likably old-fashioned and fuddy-duddy, and The Count of Monte Cristo … never quite settles on either side.” The Rotten Tomatoes movie review dataset is a corpus of movie reviews used for sentiment…

Continue Reading Tech-i-s/techis-ds-kaggle-sentiment_analysis_movie_review_NLP: Kaggle Sentiment analysis of movie review using Natural Language Processing Project

gene annotation

gene annotation 1 Hi everybody, I would like to have an advice on gene annotation. I have a list of gene names, and from this list I have to recover the gene coordinates. Can someone suggest me some tools or some library to do that ? Thank you geneannotation •…

Continue Reading gene annotation

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.

IJMS | Free Full-Text | Atorvastatin Modulates the Efficacy of Electroporation and Calcium Electrochemotherapy

Electroporation is influenced by the features of the targeted cell membranes, e.g., the cholesterol content and the surface tension of the membrane. The latter is eventually affected by the organization of actin fibers. Atorvastatin is a statin known to influence both the cholesterol content and the organization of actin. This…

Continue Reading IJMS | Free Full-Text | Atorvastatin Modulates the Efficacy of Electroporation and Calcium Electrochemotherapy

Prevent DEXSeq breaking transcripts entry when outputting to file

I have multiple DExSeq results files I want to export to tables, but I’m finding that when I output the results directly using write.table() then with large numbers of transcripts for the exon (more than 27), the output is split over two files like: ENSG00000005302 E052 139.860053137518 0.0139936600509854 6.47551836787261 0.0109370410611376…

Continue Reading Prevent DEXSeq breaking transcripts entry when outputting to file