Tag: Java

Three families of Asgard archaeal viruses identified in metagenome-assembled genomes

Liu, Y. et al. Expanded diversity of Asgard archaea and their relationships with eukaryotes. Nature 593, 553–557 (2021). CAS  PubMed  Google Scholar  Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018). PubMed  PubMed…

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Senior Software Developer (commencing immediately) at European Molecular Biology Laboratory (EMBL)

Contract Type: Staff Member Location: EMBL-EBI, Hinxton near Cambridge, UK Job Function: Senior Technical Officer (gr. 6-8) Contract Duration-Length of Time (years/months): 1 year (until grant-end date of 30/10/2023) Contract Duration-Is this renewable to 9 years?: No Advertised Grade-Grading: Grade 6 (monthly salary starting at £3,143.06 after tax plus benefits) About the team/job We are seeking…

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BAM – Job openings – Data Scientist for additive manufactruing (m/f/d) in the field of business informatics, computer science, software development, bioinformatics, engineering, data management, physics, data engineering or comparable

Section S.3 – eScience To strengthen our team in the division “eScience” in Berlin-Steglitz, starting as soon as possible, we are looking for a Data Scientist for additive manufactruing (m/f/d) in the field of business informatics, computer science, software development, bioinformatics, engineering, data management, physics, data engineering or comparable Salary…

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St. Jude Children’s Research Hospital hiring Bioinformatics Analyst in Memphis, Tennessee, United States

The Chi Lab is seeking a Systems Immunology Specialist to work on exciting projects related to immune signaling and metabolism in the St. Jude Deparment of Immunology. One of the premier pediatric research institutions in the world, St. Jude Children’s Research Hospital provides exceptional resources, a collaborative environment, and access to…

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Bioinformatics Analyst at Dana-Farber Cancer Institute in 450 Brookline Ave, Boston, MA

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute is a leader in life changing breakthroughs in cancer research and patient care. We are united in our mission of conquering cancer, HIV/AIDS and related diseases. We strive to create an inclusive, diverse, and equitable environment where we provide compassionate…

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Postdoctoral position in bioinformatics of Evo-Devo

Vous voyez une version de l’annonce optimisée pour les appareils mobiles. Annonce originale Introduction UNIL is a leading international teaching and research institution, with over 5,000 employees and 17,000 students split between its Dorigny campus, CHUV and Epalinges. As an employer, UNIL encourages excellence, individual recognition and responsibility. Presentation The…

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python 3.x – PySpark on Jupyterhub K8s || Unable to query data || Class org.apache.hadoop.fs.s3a.S3AFileSystem not found

Pyspark Version: 2.4.5 Hive Version: 1.2 Hadoop Version: 2.7 AWS-SDK Jar: 1.7.4 Hadoop-AWS: 2.7.3 When I am trying to show data I am getting Class org.apache.hadoop.fs.s3a.S3AFileSystem not found while I am passing all the information which all are required. I passed all three for this config fs.s3.aws.credentials.provider org.apache.hadoop.fs.s3a.BasicAWSCredentialsProvider com.amazonaws.auth.InstanceProfileCredentialsProvider com.amazonaws.auth.EnvironmentVariableCredentialsProvider…

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linux merge multiple files in picard

Why not use samtools? for folder in my_bam_folders/*; do samtools merge $folder.bam $folder/*.bam done In general, samtools merge can merge all the bam files in a given directory like this: samtools merge merged.bam *.bam EDIT: If samtools isn’t an option and you have to use Picard, what about something like…

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Bioinformatics Specialist I — Cancer Computational Biology —- Cancer Center in Boston, MA for MGH Institute of Health Professions

Details Posted: 05-Jun-22 Location: Boston, Massachusetts Salary: Unpaid Internal Number: 3190190-3499_1654275737 URLs: www.massgeneral.org/cancer-center/clinical-trials-and-research/center-for-cancer-research/investigators/rheinbay-lab www.massgeneral.org/cancer-center/clinical-trials-and-research/center-for-cancer-research/investigators/lawrence-lab Unique opportunity to join an interdisciplinary team bridging the Harvard Medical School, the Massachusetts General Hospital, and the Broad Institute of Harvard and MIT. The Rheinbay Lab and Lawrence Lab at the Massachusetts General Hospital Cancer…

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BBMap 38.90-GCC-10.2.0 (for BlueBEAR, BEARCloud VMs, and CaStLeS VMs)

BBMap 38.90-GCC-10.2.0 Unsupported: Use of this version of BBMap is not supported. More information on our Applications Support and Retention Policy. BBMap short read aligner, and other bioinformatic tools. Accessing BBMap 38.90-GCC-10.2.0 To load the module for BBMap 38.90-GCC-10.2.0 please use this command on the BEAR systems (BlueBEAR, BEARCloud VMs,…

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Index of /~psgendb/birchhomedir/admin/launchers/biolegato.app/Contents/Resources/local/java/TIGR/MeV_4_6_1/R-2.9.1/library/spatial/html

Name Last modified Size Description Parent Directory   –   00Index.html 2010-11-01 11:48 3.8K   Kaver.html 2010-11-01 11:48 1.9K   Kenvl.html 2010-11-01 11:48 2.2K   Kfn.html 2010-11-01 11:48 2.4K   Psim.html 2010-11-01 11:48 1.7K   SSI.html 2010-11-01 11:48 1.9K   Strauss.html 2010-11-01 11:48 2.1K   anova.trls.html 2010-11-01 11:48 1.9K  …

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Bioinformatics Remote Jobs – Find popular part time/ full time remote Bioinformatics jobs

Explore 2 recent remote Bioinformatics jobs & apply for free. Biology Breed new fish for sportfishing Hourly – Posted at 5 hours ago $19.43Hourly Jun 20, 2022Expiry We need help creating a new species of fish to the Sportfishing industries. The fish is to be stocked & produced by a…

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Index of /~psgendb/doc/local/java/MAExplorer/lib/MAERlibr/man

Name Last modified Size Description Parent Directory   –   mae.colorBased3dPlot..> 2005-02-19 16:02 1.2K   mae.colorBasedMatrix..> 2005-02-19 16:02 1.1K   mae.getCondHData.Rd 2005-02-19 16:02 897   mae.getCondVData.Rd 2005-02-19 16:02 889   mae.getVSfromHScondD..> 2005-02-19 16:02 1.6K   mae.loessPlot.Rd 2005-02-19 16:02 1.2K   mae.maXYpvalue.Rd 2005-02-19 16:02 898   mae.readHSfile.Rd 2005-02-19 16:02 1.5K  …

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Detailed differences between sambamba and samtools

3 month , My first post in the new student group , The false-positive mutation appears because duplicates mark Not enough ?, Tells the story of supplementary read It won’t be GATK MarkDuplicates Marked as duplicates The problem of . after , In response to this question , I began…

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Bioinformatics Scientist at Abterra Biosciences

Benefits pulled from the full job description Dental insurance health insurance on-site gym retirement plan Responsibilities: Develop and implement novel algorithms to support our antibody discovery, sequencing, and repertoire analysis.Work closely with molecular biologists and protein chemists to improve existing and develop novel methods.Perform analysis of internal, public, and collaborator…

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java – Calculating physico-chemical properties of amino acids in Biojava

I need to calculate the number and percentages of polar/non-polar, aliphatic/aromatic/heterocyclic amino acids in this protein sequence that I got from UNIPROT, using BioJava. I have found in the BioJava tutorial how to read the Fasta files and implemented this code. But I have no ideas how to solve this…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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Recent questions tagged fasta – Q&A

Most popular tags python javascript html java css reactjs c# php r sql arrays pandas c++ android jquery DataFrame python-3.x node.js c mysql list flutter JSON ios typescript sql-server swift string angular regex laravel excel django dictionary dart bash numpy postgresql loops oracle vba linux angularjs function for-loop spring spring-boot…

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OpenApi 3.0.3 code gen for Java Backend question

I have recently started to look at OpenApi code generator and I have a few questions that I couldn’t find an answer to with the usual resources (google and documentation mostly). What I want to generate via the components.yaml and the code generator: An interface with a couple of methods…

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Research Associate II, Bioinformatics at Sherlock Biosciences

Job details Salary $65,546 – $106,525 a year job type full-time Full job description Job description:Summary/objective: As part of this role, you will support the bioinformatics team in building a comprehensive bioinformatics software that informs the design of next generation molecular diagnosticsTogether with your mentor, you will refine and expand…

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Running fastqc

Running fastqc 1 I am trying to run fastqc from my home directory using the command line. I do not have access to the root directory. I have downloaded fastqc zip file and unzipped it. When going into the FastQC directory, the following options are available: Configuration, LICENSE_JHDF5.txt, cisd-jhdf5.jar, net…

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Mbedtls Application On Tcp

How to use mbedTLS library in Keil or IAR IDEs? I want to do an RSA encryption/decryption using my AT91SAM7S256 ARM MCU.After googling I found mbed TLS library. The IP networking interface includes TLSSockets which behave similarly to normal TCP sockets but automatically use Mbed TLS to set up a…

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Roche hiring Principal Bioinformatics Software Engineer, Java Development in Santa Clara, California, United States

This position may be based out of Santa Clara, California, USA, with remote work locations possible in The United States.Impact HealthcareRoche Sequencing is not only changing science, but we are changing lives. Our software teams are laying the groundwork for the future by developing powerful bioinformatics algorithms, data analysis tools,…

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Principal Bioinformatics Scientist I (REMOTE) job with F. Hoffmann-La Roche AG

Job Description We are seeking a committed and driven Principal Bioinformatics Scientist for our Computational Bioinformatics Research and Early Development team. We have a team of skilled bioinformatics researchers working in a highly collaborative environment with multiple internal and external teams. The work will be focused on developing novel methods…

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Manager of Bioinformatics in Chicago, IL for University of Chicago (UC)

Details Posted: 22-Apr-22 Location: Chicago, Illinois Type: Full-time Salary: Open Categories: Research – Laboratory/Non-Laboratory Staff/Administrative Location: Hyde Park Campus Job Description: Leads a team of bioinformaticians and provides technical guidance for the team to follow best practices and deliver data production timely. Collaborates cross-functionally with our user services, software engineering,…

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can`t find a path for to file

Trimmomatic – can`t find a path for to file 1 I simply need to run Trimmomatic, but he doesn`t see input files. May be you know how to deal with it? #creating variables INPUT_DIR=”path/folderinput” OUTPUT_DIR=”path/folderoutput” APPENDIX=”.fastq.gz” APPENDIX1=”_R1.fastq.gz” APPENDIX2=”_R2.fastq.gz” TRIMMOMATIC=”java -jar /home/path/trimmomatic-0.36.jar” #creating a loop for i in $INPUT_DIR/*$APPENDIX1 do FORWARD=$(basename…

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Accepted biojava-live 1:1.9.5+dfsg-1 (source all) into experimental, experimental

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Fri, 08 Apr 2022 21:21:13 +0200 Source: biojava-live Binary: libbiojava-java libbiojava-java-doc libbiojava1.9-java Architecture: source all Version: 1:1.9.5+dfsg-1 Distribution: experimental Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Pierre Gruet <p…@debian.org> Description: libbiojava-java – Java API to biological data and applications…

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[SpotBugs] htsjdk.samtools.cram.structure.CramHeader defines clone() but doesn’t implement Cloneable

Cloneable is not used very much so maybe deprecate and remove the clone() method? /cc @jmthibault79, @cmnbroad See spotbugs.readthedocs.io/en/stable/bugDescriptions.html#cn-class-defines-clone-but-doesn-t-implement-cloneable-cn-implements-clone-but-not-cloneable Part of #1267 Report: In class htsjdk.samtools.cram.structure.CramHeader In method htsjdk.samtools.cram.structure.CramHeader.clone() At CramHeader.java:[lines 80-85] Read more here: Source link

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What is ClustalW? Tutorial of How to Use ClustalW

Share Tweet Share Share Email ClustalW is a computer tool of significant importance in bioinformatics. Primarily, biologists and statisticians used it for multiple sequence alignment. Many versions of ClustalW over the development of the algorithm are available now. How to perform a search on ClustalW? ClustalW homepage 1. Go to…

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org.openapi.generator to Java client + model with oneOff in swagger

I’m currently enrolled with a spring-boot project, and they are using an API first approach which I think is great… except that this approach leads to us generating our ingoing API clients + input models, and the chosen tool org.openapi.generator 5.3.0 is really bad at it. I have an API…

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Trimmomatic/ linux system

Trimmomatic/ linux system 1 Hi all, I am trying to remove adapters and clean my RNA-seq.gz files using Trimmomatic, loaded on a Linux system (supercomputer server) Following the steps for Pair ends reads, explained in the manual (www.usadellab.org/cms/?page=trimmomatic) java -jar trimmomatic-0.39.jar PE input_forward.fq.gz input_reverse.fq.gz output_forward_paired.fq.gz output_forward_unpaired.fq.gz output_reverse_paired.fq.gz output_reverse_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True LEADING:3…

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How to merge multiple OpenAPI 3.0 specification files into one in Maven?

In a Maven project with Spring Boot, there are several OpenAPI 3.0 specification files. One spec defines all HTTP errors (errors.yml), and the components of errors.yml are referenced in other spec. I want to generate an output spec with all components of errors.yml inside. Input spec: schema: $ref: “errors.yml#/components/schemas/Error” Wished…

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google careers ADM

google data scientist certificate careers at google canada google applied jobs google hiring 2022 google ads specialist hiring hiring in google google company recruitment 2021 google frontend developer google reviewer job google philanthropy jobs machine learning developer google google bioinformatics jobs google android developer jobs google attorney jobs google pm…

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Install Jupyter Notebook on Debian 11 Bullseye Linux

Tutorial to learn the steps involve in the installation of Jupyter Notebook on Debian 11 Bullseye using command terminal. What is Jupyter Notebook? The Jupyter Project is a non-profit initiative that aims to develop and provide open-source software and open standards for interactive work. One of the most famous products…

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ChromatogramNonlinearScaler.Identity (biojava-legacy 1.9.2 API)

ChromatogramNonlinearScaler.Identity (biojava-legacy 1.9.2 API) JavaScript is disabled on your browser. Summary:  Nested |  Field |  Constr |  Method Detail:  Field |  Constr |  Method java.lang.Object org.biojava.bio.chromatogram.graphic.ChromatogramNonlinearScaler.Identity Method Summary Methods inherited from class java.lang.Object clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait Summary:  Nested |  Field |  Constr |  Method Detail:  Field |  Constr |  Method Copyright © 2020…

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SAMSequenceRecord

SAMSequenceRecord JavaScript is disabled on your browser. All Implemented Interfaces: java.io.Serializable, java.lang.Cloneable public class SAMSequenceRecord extends AbstractSAMHeaderRecord implements java.lang.Cloneable Header information about a reference sequence. Corresponds to @SQ header record in SAM text header. See Also: Serialized Form Field Summary Fields  Modifier and Type Field and Description static java.lang.String ASSEMBLY_TAG …

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Top 50 H20 interview questions and answers

H20 interview questions and answers 1) What is AutoML in H2O? H2O’s Automatic Machine Learning (AutoML) H2O is a fully open-source, distributed in-memory machine learning platform with linear scalability. … H2O AutoML can be used for automating the machine learning workflow, which includes automatic training and tuning of many models…

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net.sf.samtools.SAMFileHeader$GroupOrder java code examples | Tabnine

public void addAlignment(final SAMRecord alignment) { if (sortOrder.equals(SAMFileHeader.SortOrder.unsorted)) { if (!header.getGroupOrder().equals(SAMFileHeader.GroupOrder.none)) { throw new UnsupportedOperationException(“GroupOrder ” + header.getGroupOrder() + ” is not supported”); } writeAlignment(alignment); } else if (presorted) { assertPresorted(alignment); writeAlignment(alignment); } else { alignmentSorter.add(alignment); } } Read more here: Source link

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spring boot – How to make a synchronous call with WebClient using Open API Code Generator

Spring in RestTemplate documentation has note: As of 5.0 the class org.springframework.web.client.RestTemplate is in maintenance mode, with only minor requests for changes and bugs to be accepted going forward. Please, consider using the org.springframework.web.reactive.client.WebClient which has a more modern API and supports sync, async, and streaming scenarios docs.spring.io/spring-framework/docs/current/javadoc-api/org/springframework/web/client/RestTemplate.html When I…

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org.biojava.nbio.structure.PDBHeader.getRfree java code examples | Tabnine

mmtfDecoderInterface.setHeaderInfo(pdbHeader.getRfree(), pdbHeader.getRwork(), pdbHeader.getResolution(), pdbHeader.getTitle(), MmtfUtils.dateToIsoString(pdbHeader.getDepDate()), MmtfUtils.dateToIsoString(pdbHeader.getRelDate()), MmtfUtils.techniquesToStringArray(pdbHeader.getExperimentalTechniques())); mmtfDecoderInterface.setXtalInfo(MmtfUtils.getSpaceGroupAsString(xtalInfo.getSpaceGroup()), MmtfUtils.getUnitCellAsArray(xtalInfo), MmtfUtils.getNcsAsArray(xtalInfo.getNcsOperators())); Read more here: Source link

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Generate Server Code Using OpenAPI Generator

In this weblog, you’ll learn to generate server code utilizing the OpenAPI Generator based mostly on an OpenAPI specification. The code will likely be generated for a Spring Boot Application, however OpenAPI helps many different languages which can be utilized. 1. Introduction In November I attended JFall, the biggest sooner…

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MetricsFile

All Methods Static Methods Instance Methods Concrete Methods  Modifier and Type Method and Description void addAllMetrics(java.lang.Iterable<BEAN> beanz) Add multiple metric beans at once. void addHeader(Header h) Adds a header to the collection of metrics. void addHistogram(Histogram<HKEY> histogram) Adds a histogram to the list of histograms in the metrics file. void addMetric(BEAN bean) Adds a bean to the…

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java – GATK: HaplotypceCaller IntelPairHmm only detecting 1 thread

I can’t seem to get GATK to recognise the number of available threads. I am running GATK (4.2.4.1) in a conda environment which is part of a nextflow (v20.10.0) pipeline I’m writing. For whatever reason, I cannot get GATK to see there is more than one thread. I’ve tried different…

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File: reproducible.patch | Debian Sources

123456789101112131415 Author: Chris West <solo-debianbugs@goeswhere.com> Last-Update: Sun, 9 Apr 2017 17:36:01 UTC Bug-Debian: bugs.debian.org/859958 Description: make build reproducible — a/build.xml +++ b/build.xml @@ -403,6 +403,7 @@ doctitle=”${Name.biojava}-${version}” maxmemory=”512m”> <link href=”http://java.sun.com/j2se/1.5.0/docs/api/” offline=”false”/> + <arg value=”-notimestamp”/> <group title=”Core biological packages” packages=”org.biojava.bio:org.biojava.bio.dist:org.biojava.bio.search:org.biojava.bio.seq:org.biojava.bio.seq.db:org.biojava.bio.seq.genomic:org.biojava.bio.seq.io:org.biojava.bio.symbol:org.biojava.bio.alignment:org.biojava.directory:org.biojava.bibliography:org.biojava.bio.taxa:org.biojava.bio.seq.filter” /> Read more here: Source link

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V1DaemonSet – client-java-api 10.0.1 javadoc

Latest version of io.kubernetes:client-java-api javadoc.io/doc/io.kubernetes/client-java-api Current version 10.0.1 javadoc.io/doc/io.kubernetes/client-java-api/10.0.1 package-list path (used for javadoc generation -link option) javadoc.io/doc/io.kubernetes/client-java-api/10.0.1/package-list Read more here: Source link

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Mapping to multiple references using bbmap

So my question comes in two parts: First of all is what I’m trying to do within reason given the tools I am using? I am investigating the shuffling effects of a recombinase on a known reporter sequence which subsequently generates libraries of unique sequences. By simulating all of the…

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Urgent mini project: Creat plot in R with ggplot | R Programming Language | Statistics

Use ggplot to create a plot in R. The plot should look exactly like the sketch attached. Here is the data: X <- c(0,3) HighMP <- c(-0.021248, 0.02615) LowMP <- c(-0.001879, -0.008904) Please use Times New Roman as font for the plot. The font size should be adjustable. The color…

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GATK HaplotypeCaller with interval list

I am trying to use the -L option of GATK HaplotypeCaller to call SNPs and short InDels with in an interval list. My interval list file (top8snp.interval_list) content is as follows: 12 33029845 33030845 + rs24767598 13 40586682 40587682 + rs24748362 18 24373857 24374857 + rs8856159 21 50381146 50382146 +…

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Comparing Compiled and Interpreted Programming Languages

Only binary code can be understood and executed by computers. High–programmers use level programming languages like C, C++, Python, and Java. Because they mimic human languages and mathematical notation, such languages are easier to work with. On the other hand, Computers are unable to execute code written in a high–level…

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Senior Bioinformatics Software Developer – Bethesda

Medical Science & Computing, (MSC), a Dovel company, is seeking skilled Senior Bioinformatics Software Developers to join our team supporting our client, NCBI at the National Institutes of Health, (NIH) in Bethesda, MD. The National Center for Biotechnology Information (NCBI) is part of the National Library of Medicine (NLM) at…

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Efficiently merge two BAM files while retaining reads from only one file in overlapping regions

Efficiently merge two BAM files while retaining reads from only one file in overlapping regions 1 I have a WGS BAM file that is fairly large (>150GB) and a smaller BAM file (<5GB) with reads in a small 10Mbp region. I want to (efficiently) merge the two BAM files while…

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variant – Error running gatk HaplotypeCaller with allele specific annotations

I’ve got HaplotypeCaller working nicely in standard mode, like so: # Run haplotypcaller gatk –java-options “-Xmx4g” HaplotypeCaller –intervals “$INTERVALS” -R “$REF” -I “$OUT”/results/alignment/${SN}_sorted_marked_recalibrated.bam -O “$OUT”/results/variants/${SN}_g.vcf.gz -ERC GVCF But when I try in allele-specific mode, I get the following error. All I’ve done is add the -G annotations at the end,…

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H2O is an in-memory platform for distributed, scalable machine learning

H2O is an in-memory platform for distributed, scalable machine learning. H2O uses familiar interfaces like R, Python, Scala, Java, JSON and the Flow notebook/web interface, and works seamlessly with big data technologies like Hadoop and Spark. H2O provides implementations of many popular algorithms such as Generalized Linear Models (GLM), Gradient…

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LargeBuffer (BioJava-1.4 API)

LargeBuffer (BioJava-1.4 API) org.biojava.utils.io Class LargeBuffer java.lang.Object org.biojava.utils.io.LargeBuffer public class LargeBuffer extends Object Wrapper arround MappedByteBuffers to allow long-indexed access to files larger than 2 gigs. Author: Matthews Pocock   Method Summary  void force()              byte get()              byte get(long pos)              char getChar()              char getChar(long pos)              double getDouble()            …

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repo/gentoo.git – Official Gentoo ebuild repository

dev-java/cpptasks: Fix Javadoc generation on JDK 11+HEADmaster The ‘javadoc’ program shipped in JDK 11+ requires all classes used by the input source files to be present in the classpath passed to it. This has caused numerous other bugs alike, including 780531, 788109, and 820863. Closes: bugs.gentoo.org/831294 Signed-off-by: Yuan Liao <liaoyuan@gmail.com>…

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java – OpenApi Generator to generate parameter with @RequestBody as String

I have the following OpenApi specs: paths: /student: post: requestBody: required: true content: application/json: schema: $ref: “#/components/schemas/Student” responses: 204: components: schemas: Student: type: object properties: name: type: string school: type: string With org.openapitools.generator, it generates a controller with function like below void addStudent(@RequestBody Student student) { } Is there any…

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Question: total memory usage (–mem) exceeded the RealMemory in pcluster with SLURM

Hello, I have set RealMemory=58000 (though they are 64G instances) in the file slurm_parallelcluster_queue_partition.conf When I run the following commands: sbatch -N 1 -n 1 –mem=40000 –wrap=”srun script.sh first_task” sbatch -N 1 -n 1 –mem=40000 –wrap=”srun script.sh second_task” and more They will be assigned to single instance which lead to…

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How to convert a string to an inputstream in Bioclipse javascript editor?

In this situation we have to fall back to Java. You are trying to call the method ui.save which according to man ui.save looks like this: > man ui.save ——————————————— ui.save(String filePath, InputStream content) ——————————————— Save the content of the InputStream to the given path. So this method wants an…

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bioinformatics-data – Github Help

0 1 0 bioinformatics-data,An old Phylogenetik Project (2007) in JAVA, with (some) phylogeny, bioinformatics algorithms, matrix implementations and comparisons, PAM and BLOSUM (extract from gabriel.chandesris.free.fr/projets/Phylogenetik/ ) User: gabywald Home Page: gabriel.chandesris.free.fr/projets/Phylogenetik/ java bioinformatics biology javaswing bioinformatics-tool bioinformatics-algorithms bioinformatics-data student-project student-work student Read more here: Source link

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Trimmomatic parameters

Trimmomatic parameters 0 $java -jar /apps/eb/Trimmomatic/0.39-Java-1.8.0_144/trimmomatic-0.39.jar PE -phred33 seq1_L2_1.fq.gz seq1_L2_2.fq.gz _L2_r1_paired_fq.gz seq1_L2_r1_unpaired.fq.gz seq_L2_r2_paired.fq.gz Seq1_L2_r2_unpaired.fq.gz ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:5 Trimmomatic • 137 views • link updated 15 hours ago by GenoMax 110k • written 17 hours ago by ronny • 0 Login before adding your…

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Rockhopper’s alignment issue

Rockhopper’s alignment issue 0 Hi everyone, I’m trying to identify the operons with the Rockhopper tool but at the end of the alignment something strange happens: Aligning sequencing reads from file: SRR6757591_1.sorted.bam Total reads: 10209877 Successfully aligned reads: 9358027 92% (>NC_000913.3 Escherichia coli str. K-12 substr. MG1655, complete genome) Aligning…

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MCScanX: not found – githubmate

Hi CJ-Chen, Thanks for developing this tool. I having an issue when I try to use Quick Run MCScanX Wrapper. error log here: [Debug…All Standard Error Info will show as following:…] Curr log file:/tmp/TBtools.14595798488989250861.20210723103734.log Curr java version:11.0.11 Curr TBtools version:1.09854 Maxmum Memory for Curr TBtools: 4162846720 curVersion:1.09854:force Fetch Location:200 Factor:0.1516546094367225…

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Trying to trim last bp of several samples with BBduk at once

Trying to trim last bp of several samples with BBduk at once 1 Hi, I am trying to use BBduk to trim back my 151bp sequences to 150bp. I tried to create a loop for this so I could do one entire pool at the time, but I do not…

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Roche hiring Principal Bioinformatics Scientist I in Santa Clara, California, United States

Impact Healthcare Roche Sequencing is developing ground-breaking next-generation sequencing (NGS) products that allow scientists/clinicians powerful new avenues to investigate DNA, the blueprint of any lifeforms, in days enabling them to understand health conditions such as cancer, HIV, COVID19 and more! We are not only changing science but changing lives through…

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Problem with viewing BAM files in IGV

Problem with viewing BAM files in IGV 1 Hi everyone, I’m quite new to bioinformatics and I’m having some beginner problems with IGV. I’ve got some BAM files that were generated using the GATK best practice pipeline for SNP discovery, with BAI files located in the same directory. I’m using…

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Trouble running vcf2bam jvarkit tool

Trouble running vcf2bam jvarkit tool 2 I am trying to use the tool called vcf2bam from jvarkit on a server and I have the following 2 files: GRCh38_latest_genomic.fna – the file is of format FASTQ , and 00-common_all.vcf. I used samtools faidx and also picard CreateSequenceDictionary, but when I try…

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Chunk

Chunk JavaScript is disabled on your browser. All Implemented Interfaces: java.io.Serializable, java.lang.Cloneable, java.lang.Comparable<Chunk> public class Chunk extends java.lang.Object implements java.lang.Cloneable, java.io.Serializable, java.lang.Comparable<Chunk> A [start,stop) file pointer pairing into the BAM file, stored as a BAM file index. A chunk is represented as a single 64-bit value where the high-order 48…

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bbduk can’t read file

bbduk can’t read file 0 Hi all, When trying to filter reads using bbduk, I get the following error message: maskMiddle was disabled because useShortKmers=true Exception in thread “main” java.lang.RuntimeException: Can’t read file ‘/home/bioinf/TrainingData/SRR6197336/SRR6197336_1.fastq’ at shared.Tools.testInputFiles(Tools.java:185) at jgi.BBDuk.<init>(BBDuk.java:912) at jgi.BBDuk.main(BBDuk.java:78) This is my code: ~/Downloads/bbmap/bbduk.sh in1=~/TrainingData/SRR6197336/SRR6197336_1.fastq in2=~/TrainingData/SRR6197336/SRR6197336_2.fastq out1=~/TrainingData/reads/bbduk/SRR6197336_1_bbduk.fastq out2=~/TrainingData/reads/bbduk/SRR6197336_2_bbduk.fastq ktrim=r…

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net.sf.samtools.SAMTextHeaderCodec$ParsedHeaderLine java code examples | Tabnine

private void parsePGLine(final ParsedHeaderLine parsedHeaderLine) { assert(HeaderRecordType.PG.equals(parsedHeaderLine.getHeaderRecordType())); if (!parsedHeaderLine.requireTag(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)) { return; } final SAMProgramRecord programRecord = new SAMProgramRecord(parsedHeaderLine.removeValue(SAMProgramRecord.PROGRAM_GROUP_ID_TAG)); transferAttributes(programRecord, parsedHeaderLine.mKeyValuePairs); mFileHeader.addProgramRecord(programRecord); } Read more here: Source link

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Principal/senior Bioinformatics Scientist (Hereditary Disease) – Portola Valley

We are looking for a highly motivated, senior level bioinformatics scientist with extensive experience and interest in translational genomic research, genetic analysis of complex traits, quantitative genetics, and/or algorithm/pipeline development. This position requires experience with scientific programming, relational data systems, algorithms development, and statistical modeling. Top candidates will also have…

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GRRDUser Manual [PDF] | Documents Community Sharing

* The preview only display some random pages of manuals. You can download full content via the form below. Microsoft Word Add-In for the GenePattern Reproducible Research Document July 2009 Introduction…………………………………………………………………………………………………………………. 3 About GenePattern…………………………………………………………………………………………………… 3 How GenePattern and the GRRD Add-In Work Together…………………………………………………4 Reproducibility of Document Interactions………………………………………………………………………4 Installing and Uninstalling…

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Persistent Systems hiring Bioinformatics Data Scientist – South SFO, CA in Santa Clara, California, United States

About PersistentWe are a trusted Digital Engineering and Enterprise Modernization partner, combining deep technical expertise and industry experience to help our clients anticipate what’s next. Our offerings and proven solutions create unique competitive advantage for our clients by giving them the power to see beyond and rise above. We are…

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Pararellization in GATK 4

Pararellization in GATK 4 4 Hi all, I’m trying (and failing) to multi-thread HaplotypeCaller in GATK 4. I read in a few places online that multi-threading in GATK 4 has been made more tricky, maybe even unfeasible, but all the places where I read that seem to be more than…

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Computational Scientist-Bioinformatics in Chicago, IL for University of Chicago (UC)

  UPDATE: We are in process of fixing some issues with our job board search function. If you are experiencing any problems, we apologize for the inconvenience and thank you for your patience. Job Seekers, Welcome to HERC Jobs…

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org.intermine.sql.query.Query.addHaving java code examples | Tabnine

public void testHavingConstraintSet() throws Exception { q1 = new Query(“select table1.field1 from table1 group by table1.field1 having (table1.field1 = table1.field2 or table1.field1 = table1.field3)”); q2 = new Query(); Table t1 = new Table(“table1”); Field f1 = new Field(“field1”, t1); Field f2 = new Field(“field2”, t1); Field f3 = new Field(“field3”,…

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GATK HaplotypeCaller – Shutting down engine

00:32:48.224 INFO  HaplotypeCaller – Shutting down engine [September 17, 2021 12:32:48 AM CST] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 0.04 minutes. Runtime.totalMemory()=2398617600 java.nio.BufferUnderflowException         at java.nio.ByteBuffer.get(ByteBuffer.java:688)         at java.nio.DirectByteBuffer.get(DirectByteBuffer.java:285)         at java.nio.ByteBuffer.get(ByteBuffer.java:715)         at htsjdk.samtools.MemoryMappedFileBuffer.readBytes(MemoryMappedFileBuffer.java:34)         at…

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Gradle Build Error With Intellij

You can verify the problem is with Gradle scripts by running gradle help which executes configuration scripts but no Gradle tasks. If the error persists build. More examples on the classpath customization are available here. Tasks view and task execution. In the Eclipse IDE you can execute tasks from the…

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snpEff: annottation problem

snpEff: annottation problem 0 Hi everyone. I am using snpEff on my personal computer, and when I try to annotate a VCF file I get this error: [[0Kjava.lang.OutOfMemoryError: Java heap space[[0KM at java.util.Arrays.copyOfRange(Unknown Source)[[0KM at java.lang.String.<init>(Unknown Source)[[0KM at java.lang.StringBuilder.toString(Unknown Source)[[0KM at java.io.BufferedReader.readLine(Unknown Source)[[0KM at java.io.BufferedReader.readLine(Unknown Source)[[0KM at org.snpeff.fileIterator.LineFileIterator.readNext(LineFileIterator.java:46)[[0KM [[0K at…

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Bioinformatician I/II/III – Job posted on PostdocJobs.com

Job Description Farmington, Connecticut Apply Summary The Robinson lab is seeking a Bioinformaticician to join our team that focuses on the development of software and ontologies for biomedical research. Our team of expert biological curators, bioinformaticians, and computer scientists maintain and enhance a knowledge extraction and refinement process that delivers…

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Senior Bioinformatics Engineer | United States

Natera™ is a global leader in cell-free DNA (cfDNA) testing with a focus on women’s health, oncology, and organ health. To bolster our oncology products, we are looking for a Senior Bioinformatics Engineer to provide technical leadership and process guidance. Through collaboration between the product and development teams, the Senior…

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Beagle 5.2 Imputation Issue, understanding output

Hey everyone, I’m having some trouble with the imputation step in my GBS pipeline. I’m following the FastGBS pipeline basically as written up until this point. Before running Beagle, i’ve performed a filtering step using vcftools (though I get the same error whether or not I do this; I just…

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Bioinformatics Postdoctoral Research Associate job in Seattle, WA | Benaroya Research

Overview COMBATING IMMUNE DISEASE THROUGH GENOMICS ANALYSIS Come join our team and improve human health We need individuals to apply cutting edge big data approaches to study of the human immune system. We believe that understanding how the immune system is broken in diseases like cancer and autoimmunity will lead…

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snpEFF not able to download GRCH38 ?

snpEFF not able to download GRCH38 ? 2 HI Why snpEff not able to download GRCH38 ? Always its showing error, But its work well with GRCH37 reference. Thanks for your comments. likithreddy@Curium:~/Downloads/snpEff_latest_core/snpEff$ java -jar snpEff.jar download GRCh38.76 java.lang.RuntimeException: Property: ‘GRCh38.76.genome’ not found at org.snpeff.interval.Genome.<init>(Genome.java:106) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681) at org.snpeff.snpEffect.Config.readConfig(Config.java:649) at…

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Error in merged bam files

Error in merged bam files 0 Hello I am trying to merge unmapped and mapped bam files. I merged the bam files using the picard tool (gatk.broadinstitute.org/hc/en-us/articles/360036883871-MergeBamAlignment-Picard). I checked the merged bam using ValidateSamFile command (gatk.broadinstitute.org/hc/en-us/articles/360036854731-ValidateSamFile-Picard-) and it showed the below errors: Error Type Count ERROR:MATES_ARE_SAME_END 5496 ERROR:MISMATCH_FLAG_MATE_NEG_STRAND 5478 ERROR:MISMATCH_MATE_CIGAR_STRING…

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Higher Education Recruitment Consortium (HERC), HERC Jobs|Find Your Career Here

  UPDATE: We are in process of fixing some issues with our job board search function. If you are experiencing any problems, we apologize for the inconvenience and thank you for your patience. Job Seekers, Welcome to HERC Jobs…

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The Choice Of Most Champions

In this article, we’ll learn about XGBoost, its background, its widely accepted usage in competitions such as Kaggle’s and help you build an intuitive understanding of it by diving into the foundation of this algorithm. XGBoost XGBoost is an algorithm that is highly flexible, portable, and efficient which is based on a decision tree for ensemble learning…

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org.forester.phylogeny.data.Confidence.getValue java code examples | Tabnine

new NHXParser() ); ConfidenceAssessor.evaluate( “bootstrap”, ev0, t0, false, 1, 0, 2 ); if ( !isEqual( t0.getNode( “ab” ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { return false; if ( !isEqual( t0.getNode( “abc” ).getBranchData().getConfidence( 0 ).getValue(), 3 ) ) { return false; new NHXParser() ); ConfidenceAssessor.evaluate( “bootstrap”, ev1, t1, false, 1 );…

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Sql Server Import From Excel With Sql, Duplicate Column Names

Explore LabKey Server’s specialized tools for assay data management below and read additional documentation on the LabKey support and documentation portal. Flow. Using SQL Search you can search for the column name and find all the stored procedures where it is used. Work faster. Finding anything in the Object Explorer….

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Web Developer at European Molecular Biology Laboratory (EMBL)

About the team/job IT Services operates and supports the IT infrastructure and services at EMBL headquarters in Heidelberg and at the laboratory’s sites in Barcelona and Rome. In collaboration with the EMBL-EBI in Cambridge our team is creating and implementing a new web infrastructure for all EMBL websites. We are…

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Bioinformatics Support Specialist (Remote) at Agilent Technologies, Inc.

Agilent inspires and supports discoveries that advance the quality of life. We provide life science, diagnostic, and applied market laboratories worldwide with instruments, services, consumables, applications, and expertise. Agilent enables customers to gain the answers and insights they seek so they can do what they do best: improve the world…

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Picard CalculateHsMetrics perTargetCoverage for Novaseq bams

Picard CalculateHsMetrics perTargetCoverage for Novaseq bams 0 Hello, I would like to use Picard’s CalculateHsMetrics to calculate per target coverage for Novaseq bam files. It seems that the tool is not able to calculate mean/normalized coverage for Novaseq bams but works well with Hiseq bams. Novaseq bams report quality scores…

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HaplotypeCaller Memory Optimization

HaplotypeCaller Memory Optimization 0 When using HaplotypeCaller on GATK, is there a fixed amount of memory that works well for for the java -Xmx input, or does it scale with the size of the input bam? eg if I have a 50 GB file do I need to set -Xmx…

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BIOINFORMATICS SCIENTIST job in in Dubai United Arab Emirates

Description Overview We are looking for a highly motivated and creative bioinformatics research scientist to develop and apply innovative analytical approaches to understand the genetic modifications that drive the development and response to therapy of blood tissues. The scientist will contribute ideas to implement automate and improve existing analysis methods,…

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Would my Bachelor degree allow me to land a job? (Check the curriculum below) : bioinformatics

I thought I’d get some insight from you about my Bachelor degree in Bioinformatics (link) Just to clarify a few things, the programming languages I’ve learned through my courses are Java, Perl, bash, R, Python (to a lesser extent). Also, in the Data Mining course we basically covered most of…

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Research Scientist- Bioinformatics & Computational Biology

Position Description: Research Scientist- Bioinformatics & Computational Biology, position in Christopher S. Bond Life Science Center, University of Missouri-Columbia. Potential Start Date: November 1, 2021 Duration: 24-month initial appointment, renewable afterwards Minimum Qualifications: Applicant must have a PhD degree in Computer Science, Bioinformatics, or related field. Strong publication record, especially…

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Trimmomatic error

Trimmomatic error 1 Hi everyone. I’m trying to trim some read data but i’m getting an error message. This is my input: trimmomatic PE -threads 24 -phred 33 /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R1.fastq.gz /home/tbeckett/lustre/practice/output_data/ Filtered2S1_L3_R2.fastq.gz /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R1_un.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_p.fastq /home/tbeckett/lustre/practice/output_data/trimmed/ TrimmedFiltered2S1_L3_R2_un.fastq ILLUMINACLIP:NexteraPE-PE.fa LEADING:20 TRAILING:20 MINLEN:60 This is the error i’m getting:…

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MiXCR error with the complied cat TCR library

MiXCR error with the complied cat TCR library 0 Dear great helpers, I compiled json library for cat’s TCR using ‘repseqio’ as attached file. The command lines were as followed: $MIXCR analyze amplicon –threads 20 –library imgt –species “cat” –starting-material rna –5-end v-primers –3-end j-primers –adapters adapters-present –receptor-type tcr –region-of-interest…

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gmod prop hunt not working

I’ve let the server stay open so you can join it and test for yourself. Game Garry’s Mod. It’s just textures (and maps, if you need it) for use as an addon to Garry’s Mod. From hunting down everyday objects in Prop Hunt to strangling and trampling pigs in Open…

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foursquare dataset kaggle

Using the Foursquare API and querying for the above venues, the best locations can be shortlisted. Python, Foursquare API Location Data, Kaggle Data, Web Scraping, KMeans Clustering, Pandas, Sci-kit Learn See project. Data came from Kaggle Dataset , and it contains a few million Amazon customer reviews. I will be…

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Clinical Bioinformatics Scientist/Engineer Job in Massachusetts (MA), Career, Full Time Jobs in Novartis Pharmaceuticals

6500 – The number of associates in the Novartis Institutes for BioMedical Research (NIBR). This division is the innovation engine of Novartis, focusing on powerful new technologies that have the potential to help produce therapeutic breakthroughs for patients. We are seeking a bioinformatics scientist to coordinate the processing and…

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