Tag: Java

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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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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Can’t run java in bash script : bioinformatics

I was trying to re-use one of my old scripts for trimmomatic but I was getting error “java: command not found”. I realised that it will work if the java command is first. It stops if there is anything above it, e.g This works: #!/bin/bash java –version PATH=/media/msz/Arabidopsis_project/scripts $ ./test.sh…

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Speeding up HaplotypeCaller analysis

Speeding up HaplotypeCaller analysis 0 how can I speed up the HaplotypeCaller command running? input bam file is about 16G and running time using the below command is about 15 hours. java -Xmx64G -jar GenomeAnalysisTK.jar -nt 1 -nct 34 -T HaplotypeCaller -R Renamed.fasta -I realigned.bam -o raw_variants.g.vcf.gz -ERC GVCF GATK…

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bike sharing demand kaggle solution

06 Set bike sharing demand kaggle solution Posted at 20:36h in Notícias by Thanks for sharing. DEEP LEARNING METHODS Theano, Pylearn2 Caffe, 4i. For this reason, when we need to make a decision we often seek out the opinions of others. This is true not only for individuals but also…

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Paired-end reads reported without mates: how to play matchmaker?

Hi Everyone, I am currently looking at Acute Myeloid Leukemia (AML) paired-end WGS samples from the TARGET data ocg.cancer.gov/programs/target/target-methods#3241. A bioinformatician in our group remapped the samples from hg19 to hg38. Unfortunately, we do not have any copies of the hg19 version anymore. However, when I try to run anything…

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How to filter GATK vcf file using other programs

How to filter GATK vcf file using other programs 0 hi everyone I called variants for a WGS project using GATK (HaplotypeCaller). Now, when I want to filter that VCF file by VariantFiltration command in GATK, so the following error message appears. java.lang.NumberFormatException: For input string: “10.90” I asked my…

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Bioinformatics Scientist in Frederick, MD

Job DescriptionBioinformatics ScientistFull Time Direct Hire Remote positionAre you looking for bioinformatics work? Are you interested in joining a team of talented bioinformaticians dedicated to understanding the genetics of cancer? In this role you will:* Function as a scientific thought leader within for all aspects of GWAS and population genetics….

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Assistant Research Professor – Genomics and Bioinformatics job with City of Hope

About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…

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New Evidence for ‘Out of Africa’ Origins | Science

One of the biggest battles in human anthropology rages over whether modern humans descended from relatively recent emigrants from Africa or from several populations of early hominids, including Neandertals. Now a study of characteristic DNA sequences called “markers” in the Y chromosome adds support to the Out of Africa hypothesis….

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wont recognize the gtf or gff3 files (runtime exception)

snpeff : wont recognize the gtf or gff3 files (runtime exception) 1 Hi, I am trying to build a custom databasee for snpeff. As instructed both in the forum and snpeff instructions, I did the following; Then I added the following into snpEff.config file # BG94_1 BG94_1.genome : BG94_1 Then…

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Lab Technician (Bioinformatics) in Quantitative Stem Cell… Jobs in Barcelona, Barcelona provincia at IRB Barcelona –

Created in 2005 by the Generalitat de Catalunya (Government of Catalonia) and the University of Barcelona, IRB Barcelona is a Severo Ochoa Centre of Excellence—a seal that was awarded in 2011. The institute is devoted to conducting research of excellence in biomedicine and to transferring results to clinical practice, thus…

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Senior Bioinformatics Data Engineer – GRAIL

GRAIL is a healthcare company whose mission is to detect cancer early, when it can be cured. GRAIL is focused on alleviating the global burden of cancer by developing pioneering technology to detect and identify multiple deadly cancer types early. The company is using the power of next-generation sequencing, population-scale…

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Senior Bioinformatician / Developer (Analysis Pipelines) at Earlham Institute

Applications are invited for a Senior Bioinformatician / Developer to join the Laboratory of Dr David Swarbreck in the Digital Biology Programme at the Earlham Institute, based in Norwich, UK. Background: The Core Bioinformatics Group employ cutting edge technologies and computational approaches to deliver high-quality data analysis and develop software…

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Research Bioinformatician II – Knott Lab

Research Bioinformatician II – Knott Lab – Bioinformatics & Functional Genomics Apply Now Share Requisition # HRC0654414 The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II! This position provides excellent…

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Bioinformatics Co-Op – Spring 2022 – Remote

Job Description This is a 6-months program (might be longer not shorter)​ working full-time (40h/week). EMD Serono’s Bioinformatics group is looking for Coop students for Fall 2021/Winter 2022. The selected candidate will work on several target discovery and biomarker development projects within the Immunology and/or Immuno-Oncology therapeutic areas. An ideal…

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Image Data Specialist – Euro-BioImaging at European Molecular Biology Laboratory (EMBL)

About the team/job The Euro-BioImaging Bio-Hub hosted by the European Molecular Biology Laboratory (EMBL) is looking for a highly motivated image data specialist to technically support the Image Data Services of the European research infrastructure Euro-BioImaging ERIC (www.eurobioimaging.eu). Euro-BioImaging is building and offering image data services to the research community….

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Novogene America hiring Bioinformatics Specialist in Sacramento, California, United States

Job description Responsibilities: · Develop and maintain bioinformatics pipeline of NGS data · Research in Bioinformatics Specialty and Follow up the Frontier Trends of Life Science Research · Data mining from high throughput sequencing data generated by Novogene or other research groups. · Responsible for the maintain and improvement of…

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Seer hiring Bioinformatics Scientist in Redwood City, California, United States

At Seer, we are passionate about empowering our customers to expand scientific discoveries and achieve exceptional scientific outcomes. Our team is growing quickly as we develop innovative approaches to solve complex biological questions. And we believe the next frontier in biology is enabled through a clearer and more complete view…

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Jobs | Bioinformatics Research Center

Bioinformatics Research Associate   The successful applicant’s primary responsibilities will include database development and management, as well as design and implementation of workflows in genetics and biology in multiple languages, including R, Java, python, and React.js. The Associates will also have the opportunity to collaborate with researchers at the University…

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Genentech hiring Principal Bioinformatics Scientist I in Pleasanton, California, United States

The PositionImpact HealthcareRoche Sequencing is developing ground-breaking next-generation sequencing products that allow scientists/clinicians powerful new avenues to investigate DNA, the blueprint of any lifeforms, in days giving them the ability to understand health conditions such as cancer, HIV, COVID19 and more! We are not only changing science but changing lives…

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Bioinformatics Engineer | San Carlos, CA

Date posted: Aug 28, 2021 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 solutions, we are looking for a Bioinformatics Engineer to provide analytical and data management support for Natera’s oncology product. The Bioinformatics…

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University of Michigan, Postdoc Positions in Computational

哇,mm~ 顶啊 【 在 McKinsey (00) 的大作中提到: 】代一个朋友发,有兴趣的请直接通过下面email联系。 Post-doctoral positions in Computational Biology: Join our team to identify the functions and pathways of disease genes! Several computational biology post-doc positions are available in the newly established Functional Genomics group in the Department of Computational Medicine and Bioinformatics at the University…

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PostDoc computational biology/bioinformatics (m/f/d) (fulltime, 5 year tempory appointment), Berlin, Germany

Job:PostDoc computational biology/bioinformatics (m/f/d) (fulltime, 5 year tempory appointment), Berlin, Germany 0 The Berlin Institute of Health (BIH) JRG Computational Genome Biology is looking for a PostDoc computational biology/bioinformatics (m/f/d) (fulltime) to fill a five year temporary appointment. The position is advertised conditional on the provision of third party funds…

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Error in loading files into the GSEA software

Error in loading files into the GSEA software 0 Hi everyone I have some trouble with my RNA-seq file when I try to upload it for analysis with GSEA. I am getting the following error: Can anyone help me fix it? many thanks! —- Full Error Message —- There were…

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Output per variant and per sample heterozygosity fraction from VCF.

Output per variant and per sample heterozygosity fraction from VCF. 2 As a QC measure I would like to know the per variant and per sample heterozygosity fraction. I already used vcftools to output the missingness per variant and sample. vcftools.github.io/man_latest.html Is there any tool that can do the same…

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BioViz Connect: Web application linking CyVerse science gateway resources to genomic visualization in the Integrated Genome Browser

Abstract Genomics researchers do better work when they can interactively explore and visualize data. However, due to the vast size of experimental datasets, researchers are increasingly using powerful, cloud-based systems to process and analyze data. These remote systems, called science gateways, offer user-friendly, Web-based access to high performance computing and…

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Graduate/PhD Student Computational Biology/Bioinformatics, Berlin Institute of Health, Germany

Job:Graduate/PhD Student Computational Biology/Bioinformatics, Berlin Institute of Health, Germany 0 The Berlin Institute of Health (BIH) JRG Computational Genome Biology is looking for a PhD Student Computational Biology / Bioinformatics (m/f/d) (fulltime) to fill a three year appointment (earliest start Nov 1st, 2021). The bioinformatics group “Computational Genome Biology” of…

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the Genomic Rearrangement IDentification Software Suite

Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…

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Bioinformatics Analyst in Pittsburgh, PA

Description Purpose: The UPMC Genome Center is a clinical grade, full-service, high-throughput genome center with sequencing options designed for both clinical and research needs. We are looking for members to join our Bioinformatics team for analysis of a wide spectrum (Whole Exome/Genome Germline and Somatic, RNAseq, scRNAseq) of NGS data…

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gatk, ref and alt percentages .

gatk, ref and alt percentages . 0 Hello everyone, I need some info regarding how to get percentage of REF and ALT nucleotide sequence in my data. I am using gatk and currently not getting REF and ALT percentages . the command i am using for the gatk vcf file…

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phase_trio.sh | searchcode

phase_trio.sh | searchcode PageRenderTime 24ms CodeModel.GetById 16ms app.highlight 5ms RepoModel.GetById 1ms app.codeStats 0ms /Phase/phase_trio.sh github.com/BioinformaticsArchive/fCNV Shell |…

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Linearize fasta files

Program versions used: BBMap – v. 38.32Seqtk – v. 1.3-r106Seqkit – v. 0.8.1Perl – v. 5.16.3Python – v. 3.6.6sed – v. 2.2.2 $ time (cat Homo_sapiens.GRCh38.dna.primary_assembly.fa > /dev/null) real 0m1.050s user 0m0.002s sys 0m1.045s With BBMap – reformat.sh $ time reformat.sh -Xmx40g in=Homo_sapiens.GRCh38.dna.primary_assembly.fa fastawrap=0) java -ea -Xmx40g -cp bbmap/current/ jgi.ReformatReads…

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Senior Bioinformatician job with Barrington James

Senior Bioinformatician wanted to join a growing Bioinformatics team. Their vision is to deliver sample insight solutions to allow for more beneficial molecular insights at a quicker and more efficiently – from raw data samples to the final result.  This position will be developing the world’s leading bioinformatics software solutions. This…

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How to merge multiple patient’s vcf files (indel and snv) with different IDs?

How to merge multiple patient’s vcf files (indel and snv) with different IDs? 0 Hi all, I have some VCF files for my patients, each patient has 2 files( indel.vcf , snv.vcf) and I want to merge these file by the script bellow: java -jar gatk-package-4.2.0.0-local.jar MergeVcfs -I /PATH_TO_patient1_ID_indel.vcf -I…

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no positional argument is defined for this tool.

A USER ERROR has occurred: no positional argument is defined for this tool. 0 Hello, hope all are doing well. I am running the HaplotypeCaller command to generate the variant file by giving multiple input bam files in a single command. python3 gatk –java-options -Xmx7g HaplotypeCaller –reference ref.fasta –input file1.bam…

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issues installing pathfindR package

issues installing pathfindR package 1 Hi I am trying to use the pathfindR package to do enrichment analysis on my data. According to the vignette the package is downloaded from CRAN by install.packages(“pathfindR”) this gives the following output Installing package into �� (as �lib� is unspecified) Warning in install.packages :…

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How to give multiple input files to the gatk ?

How to give multiple input files to the gatk ? 0 Hi all, I want to use gatk-package-4.2.0.0 for updating my VCF dictionary. I use the script below for just one VCF file, and it has worked so far. java -jar gatk-package-4.2.0.0-local.jar UpdateVCFSequenceDictionary -V /PATH _TO_INPUT_FILE.vcf –sequence-dictionary /PATH_TO_DICTIONARY.dict -O /PATH_TO_OUTPUT_FILE.vcf…

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MarkduplicatesSpark How to speed-up ?

MarkduplicatesSpark How to speed-up ? 0 Hello all, I would like to know if there is any good option to speed up MarkduplicatesSpark ? I work with human genome with arround 900 millions reads (151 bp). I work on a cluster (with slurm). The command that i used is (with…

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Staff Scientist – Bioinformatics | Center for Cancer Research

Required Skills •Ph.D. in Molecular Biology, Genetics, Biomedical Sciences, or related field •Minimum of 5 years post-doctoral experience. •Good understanding of Next Generation Sequencing Data Analysis •Expertise in bulk and Single cell RNAseq, exome or panel sequencing, whole genome sequencing, copy number analyses, gene expression data analyses •Proficiency in at…

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Thermo Fisher Scientific hiring Bioinformatics Scientist in South San Francisco, California, United States

Job Title; Bioinformatics Scientist, DNA Sequencing Position Location: South San Francisco, CA As a bioinformatics scientist / engineer developing applications in oncology, personalized medicine, inherited disease, and viral/microbial genetics, you will play a key role in developing, improving, and expanding analysis solutions for next-generation DNA sequencing products. Primary responsibilities will…

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Base recalibration -Java run time error and no sequence dictionary

Base recalibration -Java run time error and no sequence dictionary 0 Hello I am stuck with base recalibration step in NGS analysis. Used this command for the base calibration step: gatk BaseRecalibrator -I sample1.bam -R gch38.fa –known-sites GCF_000001405.39 -O recal_data.table I got the following warning: WARN IndexUtils – Feature file…

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Vacancy for Bioinformatics Analyst in the USA – OYA Opportunities

Apply for Vacancy for Bioinformatics Analyst at Weill Cornell Medicine in the USA. The deadline for this job is 30th September 2021. About: Weill Cornell Medicine, officially the Joan & Sanford I. Weill Medical College of Cornell University, is the biomedical research unit and medical school of Cornell University, a…

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problem in trinity installation

problem in trinity installation 0 I am using ubunto 16.4 I tried to install trinity by following the instructions on the web. After downloading and extracting, I typed “make” the “make plugins” Then I ran trinity on test data as mentioned i.e byu typing “./runMe.sh” but following error is shown:…

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Bioinformatics Software Engineer, Cancer Genomics Research Laboratory (req2036) job with Frederick National Laboratory

PROGRAM DESCRIPTION We are seeking an enthusiastic, creative, and collaborative bioinformatics software engineer to support pipeline development and analysis for our broad portfolio of genomic studies. If you have experience designing and deploying robust, reproducible, production-quality pipelines, then come join our talented team of bioinformaticians dedicated to understanding the genetics…

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Beagple 5.2 phasing error

Beagple 5.2 phasing error 0 Hi everyone, I’m trying to phase a multi-sample (12 samples) vcf file with the first chromosome. I got this vcf after pruning with plink and recode it back to vcf. The file looks like this: 1 112 . C T . . PR GT ./….

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Error when Phasing with Beagle 5.2

Error when Phasing with Beagle 5.2 0 I’m having trouble phasing a multi-sample (9-samples) vcf file produced by gatk HaplotypeCaller with Beagle 5.2. I do not have a genetic map or reference panel. I am working with a very heterozygous group of organisms (sea urchins). When I run beagle with…

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Error when trying to run IGV on server

Error when trying to run IGV on server 1 I want to use IGV on a server so I don’t have to download bam files to my local machine. I used conda to install igvtools. When I type igvtools in the command line I get this error: Using system JDK….

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So many variants detected.

So many variants detected. 0 Dear All, I have done variant calling in Germline data that has single sample of each individual and two genes. I did following steps, but after checking results I found too many variants. After Haplotypecaller (the step 6) I found 140900 known variants, and the…

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question about running CIRI-full

question about running CIRI-full 1 I’m using ciri-full to calculate the full length sequence of circRNAs ,and I can run the test data set successfully, but I can’t run my own data running test data set: java -jar ../CIRI-full.jar Pipeline -1 test_1.fq.gz -2 test_2.fq.gz -a test_anno.gtf -r test_ref.fa -d test_output/…

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Trimming of adapters and indexes

Trimming of adapters and indexes 0 I investigate a protein which binds small DNA (<30 nt) and have a library of these small DNA. I know that adapters and indexes are from this site (5′ adapter has T instead of U). [To reach the page I want to show click…

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