Category: biotech

Problem in plotting graph or Graphics Device in the RStudio

Problem in plotting graph or Graphics Device in the RStudio 0 Hello Everyone. I’m trying to plot an Enrichissement graphic via “TCGAanalyze_EAcomplete” But when I run, nothing shows up. The console displays “null device 1” Please anyone could hepl me to fix this error. Thank you very much. below is…

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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…

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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

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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….

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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…

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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…

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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…

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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…

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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…

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

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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…

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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 •…

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Armonica Technologies closes B Round Financing

Published: Oct. 18, 2021 at 4:00 AM AKDT|Updated: 1 hours ago ALBUQUERQUE, N.M., Oct. 18, 2021 /PRNewswire/ — Armonica Technologies, Inc., a biotechnology company developing a high throughput, direct long-read DNA sequencing technology, announced that it has raised $2M in new funding.  The financing included Hamamatsu Photonics K.K. and current…

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Pondicherry University, Puducherry Wanted SRF

Research Faculty recruitment 2021 job vacancy notification announced by Pondicherry University, Puducherry for the academic year 2021-2022 for the post of SRF. Eligible candidates may apply through Email on or before 30th October 2021. Date Posted: 18th October 2021 Hiring Organization: Pondicherry University  Organization Profile: Pondicherry University was established on…

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How to test assumptions for a large number of statistical tests?

How to test assumptions for a large number of statistical tests? 0 I am running a logistic regression. The outcome is a clinical variable, there are two predictors (gene expression, hormone levels, and the interaction term between them). There is one hormone, but many genes. I am running the regression…

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Bioinformatics Data Scientist – Menlo Park

Our client is a biotech startup company in Sunnyvale comprised of industry veterans. They are well funded and developing cutting edge technology for low cost, high-performance, mass scale solutions for DNA and protein-based diagnostic testing. They are seeking a highly motivated Senior Bioinformatics Scientist to join its advanced R&D group…

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What is the orientation of the sequences in illumina paired end output file?

What is the orientation of the sequences in illumina paired end output file? 1 In a illumina paired end sequencing output file, are both the two corresponding sequences in the same orientation (like both are in 5′ to 3′) or are they in different orientaions (like one in 5′ to…

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Medical Coding Jobs – Wanted Ad Zoology, Plant Biotech& Applied Microbiology Grads | Alwarpet, Chennai

Job Details LocalitiesAlwarpet, Santhome, Seyyur, Surapet, Thillaiganga Nagar Sub RolesBio-Technology Job ID356459864 RoleMicrobiologist Hiring Company NameAchievers Spot Max Experience1 Min Experience0 Description An excellent opportunity to join as Medical Coding Specialist to perform medical coding of Case Report Form (CRF) terms using specified dictionary, thesauri and coding conventions to ensure…

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Why some CpGs start with “ch”

Why some CpGs start with “ch” 1 I am not sure why some Illumina probe ids start with ch, e.g ch.8.128185533F in the Illumina Epic methylation array. Most of the CpGs start with cg, e.g cg25251478. What are the ids starting with ch? and are these CpGs? methylation Illumina •…

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How to understand logics and statistical concepts behind limma package?

How to understand logics and statistical concepts behind limma package? 1 I want to prepare a tutorial on the logic and statistical concepts behind differential expression analysis of the limma package. My audience is biologists. So the tutorial I prepare should explain that complicated statistical concepts in simple words. What…

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Adjunct Faculty: Bioinformatics – Intro to Bioinformatics, Practical Computer Concepts for Bioinform – Baltimore

Johns Hopkins University Advanced Academic Programs Biotechnology Program Adjunct Faculty: Bioinformatics (Introduction to Bioinformatics, Practical Computer Concepts for Bioinformatics, Metagenomics) Institution Description: The Advanced Academic Programs (AAP) is a division of the Krieger School of Arts and Sciences at the Johns Hopkins University (JHU). As the nation’s oldest and one…

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US based pharmacy – we offer the best price-quality ratio for medications z y v z e a q a

Viagra as low as €0.50 Generic Viagra, containing Sildenafil Citrate, enables many men with erectile dysfunction to achieve or sustain an erect penis for sexual activity. Since becoming available Viagra has been the prime treatment for erectile dysfunction. More info Cialis as low as €0.89 Generic Cialis is a highly…

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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…

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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…

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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…

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how to plot correlation data in R

how to plot correlation data in R 0 Hi, I have got spearman’s correlation and P value like below in two separate files. Could anyone please suggest how I can make an input file after filtering strong, and significant correlation from these two files? I just want to take pVal<.01,abs(correlation)>.4….

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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…

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Bioinformatics Pipeline Developer job in Bluntisham, Huntingdonshire, Cambridgeshire

We are currently looking for a Bioinformatics Pipeline Developer to join a leading Biotech company based in the Cambridgeshire area. As the Bioinformatics Pipeline Developer you will be working on early cancer detection technology by supporting software developers and bioinformaticians KEY DUTIES AND RESPONSIBILITIES: Your duties as the Bioinformatics Pipeline…

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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…

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Question about MACS2 genome size (other organism)

Question about MACS2 genome size (other organism) 1 Hi, I’m using MACS3 to call peak with chip-seq data from Chinese hamster ovary(CHO) cells. When running the command callpeak, macs3 callpeak -t sample.bam -c Input.bam -n output -f BAM –outdir ../5.BEDfile/ -g hs -B -q 0.01 what should I type at…

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What will the the classic approach is to make pairwise comparisons between the groups in edgeR?

What will the the classic approach is to make pairwise comparisons between the groups in edgeR? 1 The edge manual I understand The classic edgeR approach is to make pairwise comparisons between the groups. For example, et <- exactTest(y, pair=c(“A”,”B”)) will find genes differentially expressed (DE) in B vs A….

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Mauve Contig Mover

Mauve Contig Mover 1 Dear all, Currently i am using “Mauve contig mover” to make an ordering of contig. I have one contig file (around 200 contig) and one reference genome file. When i am using GUI based upload its working fine. Can anybody please let me know how to…

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Understanding pilon correction on the reference sequence

Understanding pilon correction on the reference sequence 0 Hello, I need some clarification about specific kind fix made by pilon on the reference sequence: ref -GGAGTGCTCCGGGCGGGTGACCCGGCACCACCACGACAGCGCCTGCTGCTGTGGACCGA fix CGGAGTGCTCCGGGCGGGTGACCCGGCACCACCACGACAGCGCCTGCTGCTGTGGACCGA *********************************************************** ref TCAGCTGGTCCGGTTCCCGAAGGTGACTGTCTCGCAGCGTGGTCGCGTCGTCGCGACCAC fix TCAGCTGGTCCGGTTCCCGAAGGTGACTGTCTCGCAGCGTGGTCGCGTCGTCGCGACCAC ************************************************************ ref GCTGCTGCCCTGGGCCGCCTCACCGGGACGGGTCTTCCGGGTGCCGTGGTCGATCATGGA fix GCTGCTGCCCTGGGCCGCCTCACCGGGACGGGTCTTCCGGGTGCCGTGGTCGATCATGGA ************************************************************ ref CGCCGTCGACCCGGCACTGGGGCCCGTGACCGTCGGACTGGCCAACGCACCTCGTCGGGG fix CGCCGTCGACCCGGCACTGGGGCCCGTGACCGTCGGACTGGCCAACGCACCTCGTCGGGG ************************************************************ ref AACCACGCCCAATGCGGTCGGGGAATTCATTCCCTCCCGCTGCAACTGAGCACACCCCCG fix AACCACGCCCAATGCGGTCGGGGAATTCATTCCCTCCCGCTGCAACTGAGCACACCCCCG ************************************************************ ref…

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Bioinformatics Scientist, Discovery Biology – South San Francisco

Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway.Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from Stanford…

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Bioinformatics Scientist job with Hyper Recruitment Solutions (HRS)

We are currently looking for a Bioinformatics Scientist to join a leading biotech company based in the Cambridge area. As the Bioinformatics Scientist you will drive the development of computational tools and perform omics data analysis to support target identification and therapeutics development platforms KEY DUTIES AND RESPONSIBILITIES: Your duties…

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Bioinformatics Manager job with Hyper Recruitment Solutions (HRS)

We are currently looking for a Bioinformatics Manager to join a n exciting multi cultural biotech based in the Cambridge area. As the Bioinformatics Manager you will be responsible for leading and growing a highly skilled bioinformatics team KEY DUTIES AND RESPONSIBILITIES: Your duties as the Bioinformatics Manager will be…

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How can I relate bioinformatics to the social behavior of a group of people

Forum:How can I relate bioinformatics to the social behavior of a group of people 0 Hello. I have to conduct a research project about social behavior of a group of people but I need to relate it to bioinformatics / biomedical informatics. I’m have a huge struggle trying to find…

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Pseudogenes in the human genome annotation

Pseudogenes in the human genome annotation 2 Hi everyone, I was wondering if anyone if familiar of any annotation term in the human genes annotation e.g. from gencode or ensembl to be able to extract pseudogenes and separate them from non-pseudogenes. Any thoughts? Thanks in advance, Sergio human genome GRCh38…

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Residue-residue contact vs protein-protein interactions

Residue-residue contact vs protein-protein interactions 1 Hi everyone, I’m concern about the problem of predicting binary protein-protein interaction. Two proteins are defined to interact if they form a complex executing a function transiently and stably, e.g. a protein-ligand binds to a protein-receptor, homo-oligomers protein. But I notice that given two…

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Enzyme characterization and Engineering Postdoc (R2)

Job:Enzyme characterization and Engineering Postdoc (R2) 0 Context And Mission To perform characterization, bioprospecting and enzyme engineering for recycling of biobased furanic polymers Key Duties Perform molecular modeling and bioinformatics (including machine learning) on multiple enzymatics-substrate systems. Requirements Education PhD in Biochemistry, biotechnology or related field Essential Knowledge and Professional…

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Reconstruct SNP haplotypes from Illumina short reads

Reconstruct SNP haplotypes from Illumina short reads 1 I have whole genome sequencing data (Illumina paired-end 150bp) for a diverse set of highly polyploid accessions with various levels of ploidy (2n=6-16x). I would like to know if there is a method to get sequencing depths for combination of alleles that…

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Postdoc on Protease Engineering (R2) | Job Offers

Deadline: 30/11/2021 Centre / Institution: Barcelona Supercomputing Center Bioinformatics expertise: Proteomics Job description Context And Mission To perform characterization, bioprospecting and enzyme engineering for engineering PluriZymes of Proteases Key Duties Perform molecular modeling and bioinformatics (including machine learning) on multiple enzymatics-substrate systems. …

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Selection analysis based on each leaves as foreground with FastCodeML

Selection analysis based on each leaves as foreground with FastCodeML 0 I have to test the selection for each leaves in a phylogenetic tree. In normal case(with codeml), I will be running model zero for all leaves and then model 2 for each leaves as foreground (marking leaves as #1…

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Find an it job information technology careers from bioinformatics to web design

Find an it job information technology careers from bioinformatics to web design CoAxn Technology | LinkedInResponsive Web Design in Adobe XD at Denton, Texas | UloopBioinformatics Jobs, 13559 Bioinformatics Openings A dynamic combination of creativity and technical knowledge, computer science is…

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Bioinformatics QA | Santa Clara, CA

Bioinformatics QA | Santa Clara, CA | Persistent Systems, Inc. Location: Start New Search: bioinformatics scientistamerican securitynext generation sequencingcomputational biologyassay developmentngsrochepython rgenomicsbioinformaticsbiostatisticsoriginsmolecular biologydnablueprintmachine learningvisualizationphysicshivphd Persistent Systems, Inc.Santa Clara, CA Full-time Experience in Next Generation Sequencing (NGS) Seeking a talented and tech-savvy Bioinformatics QA to join our North American security practice…

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Methodologies | Connective Tissue Gene Tests

CTGT also offers Next Generation Sequencing (NGS) panels using the SureSelect and Illumina MiSeq platforms. NGS provides high throughput sequencing of many genes simultaneously and is useful for disorders associated with multiple genes. CTGT utilizes advanced technology and innovative, custom-designed software to perform next generation sequencing tests.  Our next generation…

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sanger method of dna sequencing flow chart

Flowchart Describing Assembly And Annotation Procedures The . Flow Chart Summarizing The Procedure For Identifying The Dna . Sangers Method Of Gene Sequencing Online Biology Notes . Sanger Sequencing Wikipedia . Flow Chart For The Analysis Of A Metagenome From Sequencing . Dna Sequencing Article Biotechnology Khan Academy . Flowchart…

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Looking to start a nanopore sequencing related project

Looking to start a nanopore sequencing related project 0 Hi, I am a master’s student in my last year of study and I need to do a project before I graduate. I want to do something with nanopore sequencing, and I’ve been in contact with a faculty on campus about…

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Looking for volunteer positions

Looking for volunteer positions 1 I am a Bioinformaticians (specialized in genomics) working for the NHS in a training position (called STP). This program allows me to do up to 6 weeks of work in an external lab/company/whatever in the UK or abroad. Some of my interests are programming, python,…

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Creating column that groups data from another columns

Creating column that groups data from another columns 1 Hello I have data that look like this group a b c d AO1 10 10 14 15 AO1 8 8 17 15 AO1 12 15 17 20 A02 8 5 2 8 A02 18 9 12 5 A02 8 5…

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chromoMap Error: .rowNamesDF

Hi! I am trying to run the program chromoMap. But I am getting the error: Error in `.rowNamesDF<-`(x, value = value) : invalid ‘row.names’ length My program start looks like this: library(chromoMap) chr_file_1 =read.table(“~/chr_file.txt”,sep = “t”, quote=””, stringsAsFactors=FALSE) print(chr_file_1) annot_file_1= read.table(“~/annotation_pos.txt”,sep = “t”,quote=””, stringsAsFactors=FALSE) print(annot_file_1) chromoMap( “chr_file.txt”, “annotation_pos.txt”) All input…

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Colour UMAP based on expression of multiple genes

Hi all, I was just wondering if anybody had any experience with coloring something like a UMAP made in ggplot based on the expression of multiple genes at the same time? What I want to do is something like the blend function in Seurat featureplots, but with 3 genes /…

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Agilent array in R

Agilent array in R 0 Hi, I am doing two colour agilent array in R. I followed the script but… At one stage: project is RGList so this is correct but upon putting > mage(project) Error in image.default(project) : ‘z’ musi być macierzą (“z needs to be matrix) So i…

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Can not find active_site.dat.gz in pfam ftp and got perl error Use of uninitialized value $fam_id in hash element

Can not find active_site.dat.gz in pfam ftp and got perl error Use of uninitialized value $fam_id in hash element 0 well, when I followed the Readme to install Pfam_scan, I couldn’t find active_site.dat.gz in Pfam’s ftp. In every post I check , it illustrated the file should be in ftp.ebi.ac.uk/pub/databases/Pfam/current_release/;…

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Genbank | USC Advanced Research Computing

GenBank and its collaborators receive sequences produced in laboratories throughout the world from more than 100,000 distinct organisms. GenBank has become an important database for research in biological fields and has grown in recent years at an exponential rate by doubling roughly every 18 months. To access the data below,…

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Describe what you learned from the GenBank and TAIR

Transcribed image text: Describe what you learned from the GenBank and TAIR databases about the functions of the Arabidopsis thaliana gene that is most similar to your “unknown” sequence. Your discussion should include descriptions of 1) the cell type(s), tissue(s) or organ(s) where the gene is expressed, 2) the part(s)…

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NCCC and Torrington High School Students Publish in GenBank

WINSTED, CT – October 13, 2021 – Northwestern Connecticut Community College (NCCC) Biology Studies student, Renee Dunbar, recently completed the annotation of the Hortense Bacteriophage as part of Northwestern’s NSF (National Science Foundation) funded Undergraduate Research grant supplement project. Renee worked with fellow NCCC student, Meegan Rossier, and Torrington High School…

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How to determine the cutoff of hypermutation?

How to determine the cutoff of hypermutation? 0 Hi. I know that the TMB of 10 mut/Mb is usually used as the cutoff of hypermutation. But I vaguely remember that I have read a paper, which determined the cutoff of hypermutation using a algorithm (a+1.5×b???) and finally 9.44 (probably) was…

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Statistical Geneticist – Cancer job with Paramount Recruitment

Statistical Geneticist – Cancer *Based in Oxford but flexible working options* This is a fantastic opportunity to join a rapidly growing biotechnology company who specialise in the development of innovative technologies, products and offerings for the benefit of cancer patients. They are looking for a skilled Statistical Geneticist to join…

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Protein prediction tool

Protein prediction tool 0 Hello, I would like to ask you if there is a prediction tool for stop loss mutations. I have a stop loss variant that is calculated to expand my protein for 8 more amino acids. Do you have any idea to predict it’s impact. Nikos prediction…

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bowtie2 multiple index files

bowtie2 multiple index files 1 Hi, I would like to allign short pair end reads to multiple index files. i have tried different ways to map reads such as using all index files, 1 or several index files at a time but i get an error saying file does not…

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How to run combat-seq, strange output?

I ran the **combat-seq** for my data The full program was executed, but its output is as follows I checked the code several times and I do not know where the problem is Can you help? files <-list.files(“.”,”*.count”) cnt <- lapply(files,read.delim,header=F) cnt<- lapply(files,read.delim,header=F,stringsAsFactors=F) cnt<-do.call(cbind,cnt) cnt<- cnt[,-seq(1,ncol(cnt),2)] colnames(cnt)<- sub(“.count”,””,files) batch<- samplerace…

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BioSpace hiring Bioinformatics Scientist, Discovery Biology in South San Francisco, California, United States

DescriptionSurrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from…

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Aditya Sihmar’s email & phone

We set the standard for finding emails Trusted by over 9.2 million users and 95% of the S&P 500. We had no where to begin. Scouring the web at all hours of the night wasn’t gonna cut it. RocketReach has given us a great place to start. Our workflow has…

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dna seq analysis – Banya

Dna Sequencing Data Analysis Simple Software Tools . Omicscript Pipeline For Dna Seq Data Analysis Array Suite Wiki . Dna Sequencing Data Analysis Simple Software Tools . Omicscript Pipeline For Dna Seq Data Analysis Array Suite Wiki . Dna Sequence Alignment Dna Contig Assembly Software Sequence . Dna Sequence Alignment…

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Icons of popular model organisms?

Icons of popular model organisms? 4 Is there any resource of standardized and uniformly stylized (and potentially, but not necessarily, even free) icons of popular model organisms (including E. coli and other popular unicellular organisms)? I wish to use it for making a small tabular-like panel with ~10 organisms, next…

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Metagenomics normalization for long reads

Metagenomics normalization for long reads 1 Hello everyone, I am currently working on a metagenomics analysis using ONT and I have used epi2me wimp for classification of the reads. What I want is to plot the relative abundance of each species present in the sample. Epi2me outputs a read count…

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Bioinformatics Job Fair | October 22

Job:Bioinformatics Job Fair | October 22 0 The Bioinformatics CRO will be leading a networking session at the Open Precision Medicine Conference 11AM EST to facilitate conversations between employers and job seekers in bioinformatics. Job Seekers Hear from hiring managers at CROs, biotechs, and universities, who are looking to hire…

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Data Manipulation

Data Manipulation 2 Hello everyone, I have an excel file which has three columns. In the first column there are drug names (with repetition); In the second column there are cell line names in which these drugs are tested on. The same drug names as well cell line names can…

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eQTL Analysis

eQTL Analysis 0 I have each sample expression data with gene names as .csv format and snp.txt file. I would like to find eQTL and sQTL out of them. I am new to find eQTL from above files. prediction eQTL or identification analysis • 10 views Login before adding your…

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Alignment of genomes and get statistics about alignment

Alignment of genomes and get statistics about alignment 0 Hi, I have 3 genomes: 1 reference and 2 query. I would like to know which of the 2 query is more similar to the reference. I use to use nucmer for genome alignment but I can’t find a way to…

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K-mer coverage of metgenomic data, what is the uper limit of K?

K-mer coverage of metgenomic data, what is the uper limit of K? 0 It is my understanding that k-mer coverage with regards to sequencing data is simply the distribution of k-mers across the raw sequencing reads and have nothing to do with coverage of the resulting assembly? To that end,…

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Should you normalization metagenomic data

Should you normalization metagenomic data 0 I am given to understand you should not normalize when you have a smoother coverage and expected amount of data base on BBNorms documentation. Does this mean coverage over the resulting assembly or over something else? However ,given that normalisation is often used to…

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Reliable database for true paralogs

Reliable database for true paralogs 0 Hello everyone, I have been struggling to find a database that shows the true paralogs ( I mention “true” beacause some bases present some genes as paralogs that are not truly paralogs), however despite my findings I’m not sure about their reliability. In my…

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Extracting exon neighbourhoods from the human reference genome

Extracting exon neighbourhoods from the human reference genome 0 Hi all, Starting from the GRCh38/hg38 human reference genome, I would like to scan through all the exons with an aim to extract all the neighbourhoods exon–intro–exon–intro–exon I would later like to do some operations e.g. calculating lengths and doing some…

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Lipid biomarkers: molecular tools for illuminating the history of microbial life

1. Berner, E. K. & Berner, R. A. Global Environment: Water, Air, and Geochemical Cycles (Princeton Univ. Press, 2012). 2. Cavosie, A. J., Valley, J. W. & Wilde, S. A. The oldest terrestrial mineral record: a review of 4400 to 4000 Ma detrital zircons from Jack Hills, Western Australia. Dev….

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CDC, ClinGen Partner to Develop Curated List of Important Variants for Use in NGS Genetic Testing

NEW YORK – The Centers for Disease Control and Prevention said on Monday that its Genetic Testing Reference Materials Program (GeT-RM) has partnered with the Clinical Genome Resource (ClinGen) to develop a publicly available list of 546 curated clinically important variants in 84 genes for use in next-generation sequencing genetic…

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Bioinformatics Scientist job with Aerotek

Bioinformatics Scientist Exciting opportunity to work for an early-stage, innovative biotech company, to build a pipeline of novel, T-cell receptor (TCR)-based therapeutics. £45-55k per annum Starting ASAP (ideally within 2 months) WFH / On-site in Oxford a few days per week Seeking an enthusiastic and talented…

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International Conference on DNA Sequencing and Molecular Biology ICDNASMB in January 2023 in Sydney

The International Research Conference Aims and Objectives The International Research Conference is a federated organization dedicated to bringing together a significant number of diverse scholarly events for presentation within the conference program. Events will run over a span of time during the conference depending on the number and length of…

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How to search NCBI by taxa

How to search NCBI by taxa 0 I’m currently trying to get NCBI to return all virus taxa at a specific rank with a single search query. Currently, my query: Genus[Rank] AND virus in the Taxonomy database is returning few results, where I would expect around 120 hits corresponding to…

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computationally efficient nested for loop type solution for regression

I’m trying to adapt the code below where I apply a loop type regression of 1 SNP (coded 0,1,2) against a dataframe of 150 outcome variables (metabs), giving 150 models, and extract the results of the models into a dataframe. I need to scale this up to include around 70…

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How to download UCSC bed files for exons/introns/etc

How to download UCSC bed files for exons/introns/etc 0 I’m trying to download reference annotation data –specifically bed files for exons/introns in the mm10 genome, and I saw this question here saying that you can download mm10_exons.bed file from UCSC using the Table browser tool, however I need some help…

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The population genomic structure of green turtles (Chelonia mydas) suggests a warm-water corridor for tropical marine fauna between the Atlantic and Indian oceans during the last interglacial

Alfaro-Nunez A, Bertelsen MF, Bojesen AM, Rasmussen I, Zepeda-Mendoza L, Olsen MT et al. (2014) Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles. BMC Evol Biol 14:206 PubMed  PubMed Central  Article  Google Scholar  Ali OA, O’Rourke SM, Amish SJ, Meek MH, Luikart G, Jeffres C et al….

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What is the function of dna sequencers?

Asked by: Tessie Kuhlman Score: 4.4/5 (17 votes) Sequencers. DNA sequencers play a vital role in the biotechnology industry. The ability to know the four-letter sequence of any gene or DNA segment is essential to conducting research and analyzing the genetics of individuals, organisms, plants, and animals. View full answer…

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Archive GenomeStudio projects?

Archive GenomeStudio projects? 1 I need to archive some GenomeStudio (2.0) projects. Is it possible to just zip up a folder and save it somewhere? Or does GS retain stateful information somewhere else, in which case simply unzipping an archived project and trying to open it in GS won’t work?…

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Wondering what all the fuss about CRISPR is?

One major challenge faced in gene editing is the unavailability of a proper set of guidelines Gene editing is a method where a part of DNA is inserted, deleted, modified or even replaced. The ability to edit genes has helped study and understand their function better thus giving an insight…

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Creative Biogene Offers One-Stop Customized CRISPR Based

Creative Biogene Offers One-Stop Customized CRISPR Based Microbe Genome Editing Service for global clients. New York, United States – August 18, 2021—Creative Biogene has been dedicated itself to undertaking the cause of bioscience for decades and enjoys rich experiences and expertise in CRISPR gene-editing areas. Through years of efforts and…

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ICD-10-PCS Code 0F504ZF Turquoise Health MS-DRG Manual

DRG Mapping Rules for 0F504ZF To determine how a PCS code will affect MS-DRG grouping, you must first look at the patient’s primary diagnostic code. The patient will be grouped into the first MDC that lists the primary diagnostic code in the “Assignment of Diagnosis Codes” section. From there, check…

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How convert reverse strain location to forward strain location?

How convert reverse strain location to forward strain location? 0 I’m researching for making coverage of SRY gene on male samples. However, from what I read the location of SRY gene on GrCH37 is chrY:2,654,896-2,655,723 (reverse strain). But from what I search the location of Yp11.2, the band that SRY…

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Seer-Medicare ICD-9/ICD-10

Seer-Medicare ICD-9/ICD-10 0 Can you guys please help me? I am struggling to find info from Seer-Medicare. This is my first time using this database. I am looking for ICD-9 or ICD-10 codes of the vaginal wall in Seer-Medicare. I am having trouble finding them. From ResDAC documentation, I can…

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