Tag: bash

DIRECTOR BIOINFORMATICS in Aliso Viejo California USA

Job Overview: The job’s main responsibility is to lead a bioinformatics team to collaborate with cross-functional departmental teams to build and integrate cutting edge computational solutions and applications to improve clinical diagnostics. With both technical and leadership capacities, the Director of Bioinformatics will drive bioinformatics strategy and initiatives in support…

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AlphaFold2 | DGX GPU Cluster

AlphaFold2 from DeepMind has been released as an open source application.  At UNC Research Computing Center, we are able to run AlphaFold2 in our machines to provide protein 3D structure from a chain of amino acids.  Following the steps below, we will be able to invoke AlphaFold2 in Longleaf cluster….

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Averaging across multiple columns

Averaging across multiple columns 0 Hi, I would like to average values from column 3 to 24. The data structure is as follows: #FID IID SCORE10.AVG SCORE11.AVG SCORE12.AVG SCORE13.AVG SCORE14.AVG SCORE15.AVG SCORE16.AVG SCORE17.AVG SCORE18.AVG SCORE19.AVG SCORE1.AVG SCORE20.AVG SCORE21.AVG SCORE22.AVG SCORE2.AVG SCORE3.AVG SCORE4.AVG SCORE5.AVG SCORE6.AVG SCORE7.AVG SCORE8.AVG SCORE9.AVG 4206209 2159878 7.81977e-05…

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Dry Lab Manager – Bioinformatics by Gold Group in Oxford, Oxfordshire Ref: 215263025

Dry Lab Manager – Bioinformatics Role My client is a biotechnology company developing RNA medicines. They are looking for a Dry Lab Manager for a growing Bioinformatics team. Ideally you will have a background in Bioinformatics and love all things tech including hardware, software, cloud, data and security. The Dry…

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Error during running CD-HIT

Error during running CD-HIT 0 Hi, I am running CD-HIT for very large files. Warning: Some seqs are too long, please rebuild the program with make parameter MAX_SEQ=new-maximum-length (e.g. make MAX_SEQ=10000000) Not fatal, but may affect results. I tried to define the MAX_SEQ=10000000, but I could not. I am using…

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awk syntax within GNU parallel

awk syntax within GNU parallel 0 I have bedpe files where I want to remove interchromosome mappings for each bedpe file. I am doing this using GNU parallel. Example code: parallel -j 12 “awk ‘$1==$4′ {1} > {1.}_filt.bed” ::: $path/*resort.bed Where column 1 is the chromosome read 1 maps to…

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Index of /~psgendb/local/pkg/CASAVA_v1.8.2-build

Name Last modified Size Description Parent Directory   –   CMakeCache.txt 2012-01-19 08:48 25K   CMakeFiles/ 2012-01-19 09:15 –   CTestTestfile.cmake 2012-01-19 08:48 449   Makefile 2012-01-19 08:48 28K   bash/ 2012-01-19 08:48 –   bin/ 2012-01-19 09:15 –   bootstrap/ 2012-01-19 08:30 –   c++/ 2012-01-19 08:48 –  …

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Computational Biologist, Clinical Bioinformatics – Remote

The NGS Bioinformatics Group at Dana-Farber Cancer Institute seeks a Computational Biologist to work on Profile, our institutional comprehensive precision cancer medicine initiative. The candidate will work on developing NGS bioinformatic workflows and modules for the analysis of rich and complex somatic and germline data from the Profile project and…

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Computational Biologist, Clinical Bioinformatics – Remote

The NGS Bioinformatics Group at Dana-Farber Cancer Institute seeks a Computational Biologist to work on Profile, our institutional comprehensive precision cancer medicine initiative. The candidate will work on developing NGS bioinformatic workflows and modules for the analysis of rich and complex somatic and germline data from the Profile project and…

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Problem with installing python-gi-cairo on Linux

Problem with installing python-gi-cairo on Linux 0 When I’m trying to install python-gi-cairo with Bash on Linux, I get the following message: “Some packages could not be installed. This may mean that you have requested an impossible situation, or if you are using an unstable distribution that some required packages…

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Job Application for DevOps Consultant

At ProCogia we’re passionate about developing data-driven solutions that provide highly informed answers to our clients’ most critical challenges. Our projects are varied, from Data Warehouse builds, deploying Cloud Data Solutions, Dashboarding, & building predictive models. We work with industry leading clients from various sectors including Pharmaceuticals, Telecommunications, Technology, Financial…

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Job Application for DevOps Consultant

At ProCogia we’re passionate about developing data-driven solutions that provide highly informed answers to our clients’ most critical challenges. Our projects are varied, from Data Warehouse builds, deploying Cloud Data Solutions, Dashboarding, & building predictive models. We work with industry leading clients from various sectors including Pharmaceuticals, Telecommunications, Technology, Financial…

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Error: I have no name! occurs when trying to run ~$ sudo docker run –volume – General Discussions

HiI’m a new user to linux and docker.My base OS is Linux Ubuntu 18.04.6 LTS. I have a file that I want to analyse using Docker with various programs. First I created a Dockerfile using ~$ sudo docker build -t nano_tools_debian(the # comments are just for me giving myself some…

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Advice for building lammps with SVE support on A64FX – #2 by akohlmey – LAMMPS Installation

Dear LAMMPS community, I am hoping to get some advice. I am currently trying to build and tune LLAMPS on an HPC system that uses Fujitsu’s A64FX chip. The main goal here to build with Scalable Vector Extension (SVE) support to take advantage of this CPU architecture. So far, I’ve…

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Rstudio Online Free

Listing Results Rstudio online free RStudio Cloud Preview 2 hours agoRStudio Cloud is a lightweight, cloud-based solution that allows anyone to do, share, teach and learn data science online. Analyze your data using the RStudio IDE, directly from your browser. Share projects with your team, class, workshop or the world….

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Rstudio Online Free

Listing Results Rstudio online free RStudio Cloud Preview 2 hours agoRStudio Cloud is a lightweight, cloud-based solution that allows anyone to do, share, teach and learn data science online. Analyze your data using the RStudio IDE, directly from your browser. Share projects with your team, class, workshop or the world….

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QIAGEN hiring Bioinformatics Scientist in United States

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

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Post Doc Research Fellow – Bioinformatics/Computational Biology at University of North Dakota in Grand Forks, North Dakota

Job Description: Position Information: Description UNIVERSITY OF NORTH DAKOTA SCHOOL OF MEDICINE AND HEALTH SCIENCES.   Post-Doctoral Research Fellow – Bioinformatics/computational biology, Department of Pathology, Position #00023351 A postdoctoral fellow position is currently available in the Singhal lab at School of Medicine and Health Sciences (SMHS), Department of Pathology, University of North…

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Running Assembly Jobs on the Cluster with Checkpointing

Running Assembly Jobs on the Cluster with Checkpointing NERSC Tutorial 2/12/2013 Alicia Clum How We Use Genepool? • Assembly – Fungal, Microbial, Metagenome • • • Alignments Error correction Kmer matching/counting Tool benchmarking Data preprocessing – Linker trimming, changing quality formats, changing read formats, etc • Post assembly improvement •…

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sam to bam then delete sam file

sam to bam then delete sam file 1 Hi, how can I make a loop for sam to bam then delete sam file in the same loop samtobam loop • 117 views As others have suggested, do you have a process that generates SAM output that can be piped directly…

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Trim 100bp PE sequencing to 50bp reads

Trim 100bp PE sequencing to 50bp reads 2 Hello, we’re doing some QC for future sequencing and want to have an empirical comparison of 100bp SE reads with 50bp PE reads. Starting with 100bp PE reads, how can I trim the fastq file to the first 50 bases? (i.e. retain…

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Senior Bioinformatics Pipeline Development Engineer, Liquid Biopsy

Personalis is a rapidly growing cancer genomics company transforming the development of next-generation therapies by providing more comprehensive molecular data about each patient’s cancer and immune response. Our ImmunoID NeXT Platform is enabling the development of next generation immuno-oncology therapeutics and diagnostics. Summary: You will join a team of bioinformaticians…

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Manager, Bioinformatics Verification and Validation

Personalis is a rapidly growing cancer genomics company transforming the development of next-generation therapies by providing more comprehensive molecular data about each patient’s cancer and immune response. Our ImmunoID NeXT Platform is enabling the development of next generation immuno-oncology therapeutics and diagnostics. Summary: You will join a team of bioinformaticians…

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I Won’t Disclose Vax Status Because I’ll Have to Share DNA Info Next

CNN Making some truly eyebrow-raising remarks about vaccines on Sunday, Virginia Lt. Gov.-elect Winsome Sears refused to share her vaccination status because she feels it is a “slippery slope” that will eventually lead to the disclosure of her DNA information. Sears, a rising Republican star who became both Virginia’s first…

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Winsome Sears Won’t Say If She’s Vaxxed

Virginia’s next lieutenant governor Winsome Sears has an unusual reason for not sharing her vaccination status: she was worried about “slippery slopes” and said it would soon lead to people “want[ing] to know what’s in my DNA.” Sears made the comments during an interview with CNN’s Dana Bash on State…

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Download Deep Learning with PyTorch from SourceForge.net

Deep Learning with PyTorch Overview Latest techniques in deep learning and representation learning This course concerns the latest techniques in deep learning and representation learning, focusing on supervised and unsupervised deep learning, embedding methods, metric learning, convolutional and recurrent nets, with applications to computer vision, natural language understanding, and speech…

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2. Slurm Overview

Last Updated on November 19, 2021 by wfeinstein. SLURM is a resource manager and job scheduling system developed by SchedMD. The trackable resources (TRES)   include Nodes, CPUs, Memory and  Generic Resources (GRES).  Slurm has three key functions: Allocate   resources exclusively/non-exclusive to nodes, start/execute and monitor the resources on a node, and arbitrates   pending and…

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slurm – Running batch script containing a multiple job array on multiple nodes

I’m looking to run batch script file on multiple nodes. The script file includes an array of multiple jobs. I want slurm to run each jobs on 3 nodes. I tried to give this code but the slurm is issuing this warning: Warning: can’t run 1 processes on 3 nodes,…

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slurm – Running batch script containing a multiple job array on multiple nodes

I’m looking to run batch script file on multiple nodes. The script file includes an array of multiple jobs. I want slurm to run each jobs on 3 nodes. I tried to give this code but the slurm is issuing this warning: Warning: can’t run 1 processes on 3 nodes,…

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Add Cigar string and Template Length to Read Name

Add Cigar string and Template Length to Read Name 1 Hi all, I need to convert a BAM file to Fastq format, but I don’t want to loose the Cigar and TLen information. My idea is to edit each read name in the BAM file, by appending both Cigar and…

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Personalis Senior Bioinformatics Pipeline Development Engineer

Senior Bioinformatics Pipeline Development Engineer (Remote option available) at Personalis, Inc (View all jobs) Menlo Park Personalis is a rapidly growing cancer genomics company transforming the development of next-generation therapies by providing more comprehensive molecular data about each patient’s cancer and immune response. Our ImmunoID NeXT Platform® is enabling the…

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Bash script to combine numerous output files into a spreadsheet?

Bash script to combine numerous output files into a spreadsheet? 2 I am running QUAST to check the quality of assemblies. The output is simply a .tsv file with statistics of interest. I need to do this analysis for >1000 assemblies and then compare all of the output statistics. Is…

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An Introduction to Linux, Bash Scripting, and R

Tutorial:*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R 0 Please spread to all your colleagues. Well people on this forum probably know most of the basic Linux stuff, but I am losing so much time helping others. Now they can empower themselves and step up…

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An Introduction to Linux, Bash Scripting, and R

Tutorial:*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R 0 Please spread to all your colleagues. Well people on this forum probably know most of the basic Linux stuff, but I am losing so much time helping others. Now they can empower themselves and step up…

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Senior Bioinformatics Pipeline Development Engineer at Personalis

Senior Bioinformatics Pipeline Development Engineer (Remote option available) at Personalis, Inc (View all jobs) Menlo Park Personalis is a rapidly growing cancer genomics company transforming the development of next-generation therapies by providing more comprehensive molecular data about each patient’s cancer and immune response. Our ImmunoID NeXT Platform® is enabling the…

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Database/ Application Developer at European Molecular Biology Laboratory (EMBL)

About the team/job EMBO stands for excellence in the life sciences. We support talented researchers at all stages of their careers in Europe and beyond, stimulate the exchange of scientific information, and help build a research environment where scientists can achieve their best work. EMBO is an international non-profit organisation….

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[slurm-users] Warning: can’t honor –ntasks-per-node

Hi, If I submit this script: #!/bin/bash #SBATCH –get-user-env #SBATCH -p slims #SBATCH -N 2 #SBATCH -n 40 #SBATCH –ntasks-per-node=20 #SBATCH -o log #SBATCH -e log /bin/env srun hostname I get the warning: “can’t honor –ntasks-per-node set to 20 which doesn’t match the requested tasks 40 with the number of requested nodes 1. Ignoring –ntasks-per-node”. This is strange, since…

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Assistant/Associate Teaching Professor job with Northeastern University

Assistant/Associate Teaching Professor About Northeastern Founded in 1898, Northeastern is a global research university and the recognized leader in experience-driven lifelong learning. Our world-renowned experiential approach empowers our students, faculty, alumni, and partners to create impact far beyond the confines of discipline, degree, and campus. Our locations—in Boston; Charlotte, North…

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Assistant/Associate Teaching Professor job with Northeastern University

Assistant/Associate Teaching Professor About Northeastern Founded in 1898, Northeastern is a global research university and the recognized leader in experience-driven lifelong learning. Our world-renowned experiential approach empowers our students, faculty, alumni, and partners to create impact far beyond the confines of discipline, degree, and campus. Our locations—in Boston; Charlotte, North…

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[slurm-users] Unable to start slurmd service

Thanks for the quick reply.   check if munge is working properly   root@ecpsinf01:~# munge -n | ssh ecpsc10 unmunge Warning: the ECDSA host key for ‘ecpsc10’ differs from the key for the IP address ‘128.178.242.136’ Offending key for IP in /root/.ssh/known_hosts:5 Matching host key in /root/.ssh/known_hosts:28 Are you sure…

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Bioinformatics NGS Data Analyst position in Andover, Massachusetts

Job Description: Position Summary: The qualified candidate will join the Analytical Research and Development Microbiology and Strategy Testing organization in Andover, MA, a QC (GMP) laboratory that supports biotherapeutic clinical manufacturing. Candidate will report directly to Microbiology Group Leader (Principal Scientist, Ph.D.). We are recruiting an expert…

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Bash loop, count for Chromopainter script

Hello, I need to create a loop to make 2 variables (numerical) increase, one according to the other and all related to a job I have to send to a cluster. Basically I have to create various groups, and these groups are defined by these 2 variables; for instance 1st…

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SLURM batch spawner failing with client process running, config issue – JupyterHub

I am running a slurm cluster and running batchspawner, but the spawned server does not communicate with the frontend server and keeps getting killed off. c = get_config() import batchspawner import wrapspawner c.JupyterHub.ip = ‘0.0.0.0’ c.JupyterHub.hub_ip = ‘0.0.0.0’ c.JupyterHub.hub_connect_ip = ‘server_ip’ c.JupyterHub.spawner_class=”wrapspawner.ProfilesSpawner” c.Spawner.http_timeout = 60 c.BatchSpawnerBase.req_nprocs=”1″ c.BatchSpawnerBase.ip = ‘server_ip’ c.BatchSpawnerBase.req_runtime=”12:00:00″…

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SLURM batch spawner failing with client process running, config issue – JupyterHub

I am running a slurm cluster and running batchspawner, but the spawned server does not communicate with the frontend server and keeps getting killed off. c = get_config() import batchspawner import wrapspawner c.JupyterHub.ip = ‘0.0.0.0’ c.JupyterHub.hub_ip = ‘0.0.0.0’ c.JupyterHub.hub_connect_ip = ‘server_ip’ c.JupyterHub.spawner_class=”wrapspawner.ProfilesSpawner” c.Spawner.http_timeout = 60 c.BatchSpawnerBase.req_nprocs=”1″ c.BatchSpawnerBase.ip = ‘server_ip’ c.BatchSpawnerBase.req_runtime=”12:00:00″…

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Use stdin from within R studio

Presumably, Rstudio is redirecting stdin, so that it cannot be properly accessed as “stdin” or “/dev/stdin” any longer. However, stdin() still works. ,I only found the followin so far How to input EOF in stdin in R? but no help there – had to kill R-studio., Stack Overflow for Teams…

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How to compile Java files in bash?

How to compile Java files in bash? 0 Hi everyone, Am very brand new dealing with java and biojava. Am working on a project to calculate codon adaptation index CAI using java and biojava following this tutorial “www.ihes.fr/~carbone/materials/description.html“. but errors are arising while trying to compile the two java files:…

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Use slurm job id – Pretag

1 Note, using –parsable flag you might get a comma separated list. From the man page of sbatch: –parsable Outputs only the job id number and the cluster name if present. The values are separated by a semicolon. Errors will still be displayed. – Stefan Aug 7 ’20 at 9:56 ,The…

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How to customize the output of my BLASTP output tabular form

I’m trying to align the output of I got previously to against the swissprot database, and I need to have an output in tabular form with -qseqid -sacc -qlen -slen -length -nident -pident -evalue -stitleand I want to set the evalue less than 1e-10. Here is my code : #!/usr/bin/env…

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From Zero To Hero: Best Practices For Setting Up Rstudio Team In The Cloud

Learn best practices for setting up the entire Rstudio team infrastructure – Server Pro, Connect, Package Manager from the perspective of a data scientist and for a data science audience – especially those who have never worked with servers, AWS, or bash. This talk will also be applicable to data…

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segmentation fault in Bayenv2

I think I solved the problem, you need to add a “-o” flag with an output file name. I think it has to do with trying to use some local environment variable that isn’t defined/restricted on the cluster but not if you run it on desktop. Good luck! -edit: to…

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[lammps-users] Problem with Reax – LAMMPS Mailing List Mirror

Hi everyone, I hope you are fine. I’m using lammps-29Sep2021 on Linux Bash Shell in Windows 10. I want to use the Reax force field, so installed the ReaxFF package, but I got this error: ERROR**:** Unrecognized pair style ‘reax/c’ is part of the USER-REAXC package, which is not enabled…

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hpc – Submit OpenMPI job via Slurm REST API failed

Here is my job script content: #!/bin/bash #SBATCH –partition=compute #SBATCH –job-name=demo #SBATCH –output=job.%j.out #SBATCH –error=job.%j.err #SBATCH -N 3 #SBATCH –ntasks-per-node=1 #SBATCH –export=ALL srun –mpi=pmi2 -n 3 hostname When I submit this job via sbatch, it runs to completion and return hostname of my nodes SUCCESSFULLY. But if I submit via…

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Remote — Bioinformatics Scientist at Theery

JOB OVERVIEW: The job’s main responsibility is to collaborate with biologists, bioinformaticians, and clinicians to design, validate, and maintain bioinformatics pipelines and applications. Duties and Responsibilities: Provide bioinformatics support to R&D by analyzing and interpreting NGS data Validate new assays and clinical product development Perform NGS data analysis and QA/QC…

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to grep pattern

to grep pattern 1 I am interested to grep the line only containing the word “gene” present at column 3 of this following file but this word is also present at each line in column 9 of this file. Please any suggestion to use the grep in bash/linux and select…

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Why does write.ped remove the first locus?

Why does write.ped remove the first locus? 0 In order to get a VCF file from genind, I am going through hierfstat function write.ped() and then with plink I convert the result to vcf. This is my code (apologies, but I cannot provide a reproducible data for this particular scenario):…

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Scientific Solutions Architect (Bioinformatics) – it-jobs-switzerland.ch

This is a version of the job ad optimized for mobile devices. Show original job ad     About Idorsia Pharmaceuticals Ltd Idorsia Ltd is reaching out for more – We have more ideas, we see more opportunities and we want to help more patients. In order to achieve this,…

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deeptools reference-point center

deeptools reference-point center 0 Hi, For some reason using deeptools computematrix reference-point center I get instead of TSS and TSE positions I am getting one mark that says center. I’m not sure what is causing the issue? computeMatrix reference-point -p 1 –referencePoint center -R bedfiles -S wigfiles –binSize 5000 -b…

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Conda activate not working : kaggle

Hi everyone, I’m new to Kaggle and I’m trying to use it for my Bachelor’s degree thesis. However when I try to activate my conda environment it runs into an error: CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’. To initialize your shell, run $ conda…

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How do I activate a conda environment in Kaggle? : deeplearning

Hi everyone, I’m pretty new at this stuff, especially with Kaggle, and I’m trying to activate a conda environment with the conda activate command. However, it comes out with this error: CommandNotFoundError: Your shell has not been properly configured to use ‘conda activate’. To initialize your shell, run $ conda…

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Read eds files ABI 7500 FAST multicomponent_data.txt

Read eds files ABI 7500 FAST multicomponent_data.txt 0 Hello Biostars comunity, Is there any open tool to read multicomponent_data.txt files in R, Python, or Bash (ABI 7500 Fast)? I found this tool, however, the files I have do not have an XML multicomponent file, only multicomponent_data.txt files. ROX and FAM…

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Help installing Bioawk

Help installing Bioawk 1 Hello I’ve been trying to install bioawk on my ubuntu system however I’ve come into a few issues. in my user/bin directory which I’ve cloned the directory into sudo git clone github.com/lh3/bioawk.git cd bioawk/ sudo make ./bioawk ./bioawk returns usage: ./bioawk [-F fs] [-v var=value] [-c…

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Recent activity – OStack Q&A-Knowledge Sharing Community

Recent activity – OStack Q&A-Knowledge Sharing Community     I have 2 samples Mocha web tests which I’m trying to run using Velocity. For some reason, client-side tests under the /tests/mocha/client … lib packages server tests mocha client server Thoughts ? See Question&Answers more detail:os…     I’m trying to find a way to…

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Technical officer in Bioinformatics (m/f) at LNS

TECHNICAL OFFICER IN BIOINFORMATICS (M/F) Type of contract: Full-time and determined duration contract (CDD) The Laboratoire national de santé (Luxembourg public institution) is recruiting a Technical officer in Bioinformatics (m/f) for the Department of Microbiology in a full time position (40h/week) with a fixed-term contract of 12 months (ending 30 september 2022). About the Laboratoire…

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How To Run An R Script From Within Rstudio’S Built-In R Console?

2.1 Starting RStudio on the university network. Click on the Windows 10 icon in the bottom left corner of the screen then search the list of programs and click. Some Examples on basic concepts of R programming. We have provided working source code on all these examples listed below. However…

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SwarmSpawner — JupyterHub can’t connect to user servers – JupyterHub

I’m trying to setup a jupyterhub using dockerspawner.SwarmSpawner to distribute user servers among multiple compute nodes in a docker swarm. I’m having trouble spawning user servers and I’m not sure whether it’s a bug or a missing configuration option. The hub is able to spawn the user servers and the…

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Assigning variables programmatically for bwa-mem

Assigning variables programmatically for bwa-mem 1 I have the following script: bwa mem -t 10 -R “@RGtID:xxxtSM:xxxxtLB:LB-1tPU:xxxtPL:ILLUMINA” ref_genome.fa sample_1_1.fastq sample_1_2.fastq | samtools view -@ 10 -b – | samtools s sort -@ 10 -o sample_1.bam I also have a spreadsheet with a column for the forward reads (sample 1, sample…

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Samtools depth error in bash script

Samtools depth error in bash script 0 Hi! I wrote a bash script to run Samtools depth, but it gives the following error: /storage1/kaman/onceta/cover/brca12_uniq.bed /storage1/kaman/onceta/cover/ENIGMA_uniq.bed /storage1/kaman/onceta/cover/bam/26m_s67_l001_r1_001_alignment [bed_read] Parse error reading “26m_s67_l001_r1_001_alignment.bam” at line 1 samtools depth: Could not read file “26m_s67_l001_r1_001_alignment.bam” The script looks like this brca12_bed= realpath brca12_uniq.bed enigma_bed=…

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Could you give me some advices about how to edit a file?

Could you give me some advices about how to edit a file? 0 Hi, all. I would like to edit the string “containing” status from the file as following. before Y43D4A.5b WBGene00012791 status=Partially_confirmed F27E5.1 WBGene00009192 asah-2 M04G12.4b WBGene00010868 somi-1 M04G12.4b WBGene00010868 somi-1 Y75B7AR.1 WBGene00022287 status=Confirmed after $ head after.file Y43D4A.5b…

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Using R in Conda

(DISCLAIMER: some of the steps described here explicitly go against the official conda installation & usage instructions; beginners should follow the official guides instead before trying any of these steps, and fully understand what these steps are doing before trying them out) Thanks for the detailed notes. I have never…

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Job: Senior Bioinformatics Scientist – (28180-JOB) at Illumina Singapore Pte Ltd Singapore

Job Description Basic Function and Scope of the Position: As a Sr. Bioinformatics Scientist, your primary responsibility is to enable the data analysis and processing and successfully delivery of data within a cloud system to meet project based KPIs for to client(s) in Singapore, as part of large and strategic…

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Genome Preparation for SynNet-Pipeline

Hi, I wanted to use this pipeline to do a synteny analysis between a couple of genomes. I’m using sequences from NCBI as well as phytozome (cds and GFF files). One of the requirements for the pipeline is that I shorten the gene names and add unique identifiers. This is…

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Job: Sr Bioinformatics Software Engineer (Dragen)-

Job Description Position Summary:We are looking for a highly driven and talented bioinformatics engineer or software engineer to join the DRAGEN verification Team.The team focus on developing tools to analyze large genomic datasets, setting up a CI/CD and automated testing infrastructure and improving the databases and websites that we use…

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Bam File Average Coverage Depth Changes After Fixmate

Bam File Average Coverage Depth Changes After Fixmate 0 I am sure this is a silly question. I have a BAM file and when I compute average coverage using samtools depth -a *BAM file* | awk ‘{sum+=$3} END { print “Average = “,sum/NR}’ I get 13.4499 Then I sort by…

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BioSpace hiring Bioinformatics Analyst – Data Scientists in Rockville, Maryland, United States

Program DescriptionThe Frederick National Laboratory is dedicated to improving human health through the discovery and innovation in the biomedical sciences, focusing on cancer, AIDS and emerging infectious diseases. With leading science and technology, the laboratory performs basic research, supports clinical trials and drug development, develops and applies next-generation technologies to…

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print next line IF statement

print next line IF statement 0 Heys, I’m working with a fasta file with several individuals and I want to split them by a particular coordinate in the genome. I wrote this: for i in $(cat fasta.file); do if [[ $i == *”coordinate”* ]]; then echo $i AND THE NEXT…

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Low mapping frequency on STAR

Low mapping frequency on STAR 0 Hi all, I’ve been trying to re-map some RNA-seq fasta files to mm39 using STAR. I was told by the sequencing facility who ran the requencing for me that when they mapped the reads onto mm10 using BWA MEM their mapping frequency for each…

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output as input new function

output as input new function 0 Heys, I’m working with samtools view to check a specific region from my bam file and I would like to convert that region into fasta piping it to angsd. However, I’m not being able to do it. How should I indicate I want the…

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A bash question

A bash question 0 Hi, I have a set of human exome data sequenced with Agilent Sureselect XT HS2. I am following the Best practice document www.agilent.com/cs/library/software/public/AGeNTBestPractices.pdf On p.3 the example for bwa, just want to check if this is correct before starting the long process for alignment. especially the…

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How to get protein ID from gene ID (batch entrez)

How to get protein ID from gene ID (batch entrez) 1 Hi can someone suggest me How to get protein ID from gene ID (batch entrez). I have hundreds of gene name like  AaeL_AAEL004207  with gene ID 5564359. Manually we can get the protein ID one by one, the problem I have…

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STAR alignment speed?

STAR alignment speed? 1 Hello, I’m currently running some RNA-seq experiment alignments on a server with STAR. After about two hours, looking at the head of the Log.progress.out file, I am getting a result like this: My total read count for the sample is ~80,000,000 reads. Does this mean that…

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Help writing this shell for salmon quantification?

Noob: Help writing this shell for salmon quantification? 0 I am a total noob here trying to analyze my RNA seq data. I’ve just started trying to use Salmon for my quantifications, and wanted to use their suggested script for running all of the samples in a loop instead of…

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CSIRO Postdoctoral Fellowship in Transformational Bioinformatics at CSIRO Australia

The Opportunity   Kick-start your research career in Bioinformatics Contribute to the development of genome-based analytics and clinical applications Join CSIRO – Australia’s leading scientific research organisation!    CSIRO Early Research Career (CERC) Postdoctoral Fellowships provide opportunities to scientists and engineers who have completed their doctorate and have less than three years…

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Sliding window plot using Python

Sliding window plot using Python 1 I want to plot the number of positions in a sliding window of 1000 and a step of 20 for each sample (A-D). Interpretation: 1: position exists; NA: position does not exist. I have tested a dozen tools in bash, R and other but…

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Bioinformatics Scientist II – 64019 Jobs in Philadelphia, PA – Children’s Hospital of Philadelphia

Location: LOC_ROBERTS-Roberts Ctr Pediatric Research Req ID: 113752 Shift: Days Employment Status: Regular – Full Time Job Summary The Bioinformatics Unit (BIXU) within the Center for Data Driven Discovery (D3b) at The Children’s Hospital of Philadelphia (CHOP) is seeking a level II Bioinformatics Scientist to join our over 30 professional…

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Bioinformatics Scientist (Genome) in Bethesda, MD

Position Objective: Provide services as a Bioinformatics Scientist in support of the overall functions of the National Human Genome Research Institute (NHGRI) within the National Institutes of Health (NIH). Duties and Responsibilities: + Generate and optimize programs and scripts for the analysis of data; create programs and algorithms and develop…

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Junior Bioinformatician at the Lymphoma Genomic Laboratory

Junior Bioinformatician at the Lymphoma Genomic Laboratory Open position Junior Bioinformatician at the Lymphoma Genomic Laboratory Institute of Oncology Research (IOR) Bellinzona, Switzerland www.ior.usi.ch www.ior.usi.ch The Institute of Oncology Research (IOR) in Bellinzona, Switzerland, is a rapidly evolving,leading center for basic and translational research in oncology in Europe.IOR is affiliated…

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StringTie creates .tsv value that has null values for every gene id

Isoform Analysis: StringTie creates .tsv value that has null values for every gene id 0 Hi everyone, I am new to bioinformatics and Biostars as a whole. I am doing isoform analysis on some samples and I’ve come across a problem. The following code is what I used for StringTie….

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Trimming Illumina universal adapters using cutadapt proving insufficient

TL;DR: I have high universal Illumina adapter content in my paired-end RNA-seq reads and trimming with both the original sequence and reverse complement of the universal adapter did not completely remove the adapter content and was only effective for the R2 reads. I am trying to trim adapter sequences from…

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Showing off skills for job hunting : bioinformatics

Am I screwing up by not showing off more Python skills in my code base for job applications? I have my BS in molecular biology and have worked in academic labs for about three years now, and I’m looking to move into industry jobs in bioinformatics. Over the past 3…

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Is it possible to delete part of the header string?

Is it possible to delete part of the header string? 2 Hi, all. I would like to remove “locus=” and “gene=” from headers of fasta as following. I used tr, but the other strings disappeared, too. Before; >3R5.1a wormpep=CE24758 gene=WBGene00007065 locus=pot-3 insdc=CAA21777.2 product=”POT1PC domain-containing protein” >2RSSE.1a wormpep=CE32785 gene=WBGene00007064 locus=rga-9 insdc=CCD61138.1…

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Would you please give me some advices about how to change header?

Would you please give me some advices about how to change header? 2 Hi, all. I would like to edit headers from fasta. I have fasta with random header as following(headers are separated by space); >3R5.1a wormpep=CE24758 gene=WBGene00007065 locus=pot-3 status=Confirmed uniprot=G5EFG7 insdc=CAA21777.2 product=”POT1PC domain-containing protein” >2RSSE.1a wormpep=CE32785 gene=WBGene00007064 locus=rga-9 status=Confirmed…

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11th Place Solution of Kaggle Global Wheat Detection

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

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Technical Support Specialist – BioInformatics – Invitae

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

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

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

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Technical Support Specialist – BioInformatics – Invitae (Formerly ArcherDx)

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

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FASTQ to VCF pipeline question

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

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why Unable to establish SSL connection

why Unable to establish SSL connection 0 I want to install UCSC The Genome Browser in the Cloud (GBiC) on the server. After typing sudo bash browserSetup.sh install I get the following error –2021-10-18 10:19:21– raw.githubusercontent.com/paulfitz/mysql-connector-c/master/include/my_config.h Resolving raw.githubusercontent.com (raw.githubusercontent.com)… 185.199.110.133, 185.199.109.133, 185.199.111.133, … Connecting to raw.githubusercontent.com (raw.githubusercontent.com)|185.199.110.133|:443… connected. Unable to…

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Technical Support Specialist – BioInformatics at Invitae

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

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MethylDackel Error running on HPC server

Hello, I am trying to analyze data for RRBS (reduced representation bisulfite sequencing) and want to use BWA-METH for alignment. I also ran Bismark, but bismark output only shows mapping efficiency of 33.8% while BWA-METH shows 99.8% mapping efficiency (paired-end). So, I converted .sam to .bam with samtools and tried…

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