Category: bash

Tophat running error

Tophat running error 1 Hello, I’m trying to run tophat and I’m getting the following error that I don’t know how to fix it. Appreciate any help. [2018-05-11 11:14:58] Checking for Bowtie Bowtie version: 2.2.9.0 [2018-05-11 11:14:58] Checking for Bowtie index files (genome).. [2018-05-11 11:14:58] Checking for reference FASTA file…

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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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[Bug 1786013] Autopkgtest regression report (linux-meta-hwe-5.13/5.13.0.22.22~20.04.9)

All autopkgtests for the newly accepted linux-meta-hwe-5.13 (5.13.0.22.22~20.04.9) for focal have finished running. The following regressions have been reported in tests triggered by the package: systemd/245.4-4ubuntu3.13 (ppc64el, s390x, amd64) nvidia-graphics-drivers-340/340.108-0ubuntu5.20.04.2 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

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[Kernel-packages] [Bug 1786013] Autopkgtest regression report (linux-meta-hwe-5.11/5.11.0.41.45~20.04.19)

All autopkgtests for the newly accepted linux-meta-hwe-5.11 (5.11.0.41.45~20.04.19) for focal have finished running. The following regressions have been reported in tests triggered by the package: systemd/245.4-4ubuntu3.13 (amd64, ppc64el, s390x) nvidia-graphics-drivers-340/340.108-0ubuntu5.20.04.2 (amd64) Please visit the excuses page listed below and investigate the failures, proceeding afterwards as per the StableReleaseUpdates policy regarding…

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g++ – Wrong compiler while installing package that uses pytorch

I am installing nnDetection framework. After cloning repository and executing pip install -e . i get an error about wrong compiler. Your compiler (icpc) is not compatible with the compiler Pytorch was built with for this platform, which is g++ on linux. Please use g++ to to compile your extension….

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Slurm – Run:AI

What Is Slurm? Slurm is a system for managing and scheduling Linux clusters. It is open source, fault tolerant and scalable, suitable for clusters of various sizes. When Slurm is implemented, it can perform these tasks: Assign a user to a compute node. The access provided can be exclusive, with…

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Using VEP to get gnomAD frequencies

Hi all, I am using Ensembl VEP (command line) to annotate a VCF I have. I am specifically looking for gnomAD allele frequencies, which is fairly straight forward to do, technically speaking. However, the data looks off in some cases. For example, when I pass in: 10 69408929 COSM3751912 A…

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Using VEP to get gnomAD frequencies

Hi all, I am using Ensembl VEP (command line) to annotate a VCF I have. I am specifically looking for gnomAD allele frequencies, which is fairly straight forward to do, technically speaking. However, the data looks off in some cases. For example, when I pass in: 10 69408929 COSM3751912 A…

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Postdoctoral Research Associate / Fellow in Bioinformatics at University of Exeter

This full-time post is available immediately on a fixed term basis until 31 December 2024. The post The College wishes to recruit either a Postdoctoral Research Associate or Fellow in Bionformatics to support the work of Professor Austin Smith. This Medical Research Council and European Research Council funded post is available…

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r – GDCprepare() returns Error in function (classes, fdef, mtable)

I have downloaded Proteome Profiling data from the TCGA-LGG project with the Bioconductor package TCGAbiolinks. Then I have the following error when running GDCprepare: library(“TCGAbiolinks”) query_lgg = GDCquery( project = “TCGA-LGG”, data.category = “Proteome Profiling”, sample.type = “Primary Tumor”, legacy = FALSE) #> ————————————– #> o GDCquery: Searching in GDC…

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Active Pharmaceutical Ingredients from Brazilian Pharmacopeia in PDBQT format, for docking with AutoDock e Vina Tools

Published: 11 November 2021| Version 2 | DOI: 10.17632/dp3f425kkf.2 Contributors: Description Active Pharmaceutical Ingredients (APIs) are molecules that can be used for the manufacturing of Drugs. The Brazilian Health Regulatory Agency (Agência Nacional de Vigilância Sanitária) is responsible for the oversight and approval of production and distribution of all drugs…

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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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Sciclone took too long

Sciclone took too long 1 Dear Chris, I was trying sciclone on my data and it took one day and it was [1] “checking input data…” [1] “Not all variants fall within a provided copy number region. The copy number of these variants is assumed to be 2.” [1] “Not…

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Download RStudio 2021.09.1 Free – FileCombo

Additional Information Take control of your R for Windows code! RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging, and workspace management. RStudio is available in open source and commercial…

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RStudio Administrator Jobs in Across India at IBS Group

Project Description Luxoft is seeking entrepreneurial, dedicated, and motivated employees that are interested in joining a fast-paced Enterprise IT Architecture and Software Development Team. The ideal candidates will be involved in all aspects of RStudio Administration. Responsibilities Manage individual and departmental R and RStudio installationsAutomate R and RStudio package installationsDefining…

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Iterating over several PDB files in ProDy module

Dear all, I have been using the Prody module ESSA (prody.csb.pitt.edu/tutorials/essa_tutorial/index.html) for single proteins by directly retrieving them from the PDB. This worked fine and as described in the tutorial they provide. Now I would like to extend this and do the same calculation on ~200 structures by iterating over…

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mm39 genePred file

mm39 genePred file 1 Hello, i need a gene annotation file for the mm39 mouse genome in the genePred format. I found that there is a utility which can convert the information from the gtf format. However, where I would download the gtf file it says that it was created…

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An RStudio Addin to Help Move the Default Branch of Your GitHub Repos

Change the default branch of your GitHub repositories, from inside RStudio. Installation You can install the development version of branchMover from GitHub with: # install.packages(“devtools”) devtools::install_github(“gadenbuie/branchMover”) The app uses the usethis and gh packages. You need to configure gh with a Personal Access Token to be able to authenticate with…

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Piping bowtie2 output directly into BAM

Piping bowtie2 output directly into BAM 1 I am using bowtie2, and due to the size of the SAM output, I would like to entirely avoid the SAM file, and pipe the results into samtools to convert the output to a BAM file. I am getting a little bit hung…

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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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Happy Birthday, TensorFlow

Even if you are remotely connected to the tech world, you must have heard or read about Google’s TensorFlow. This immensely popular and loved platform celebrated its sixth birthday on Tuesday since its initial release in 2015. Though developed by the Google brain team at first for internal use, its…

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RSeQC confusing output – Half fails to determine, half is reverse strand

RSeQC confusing output – Half fails to determine, half is reverse strand 0 Hello, I am checking the strandness of a sample using infer_experiment.py and I got a pretty confusing result (for me). infer_experiment.py -i sample_Aligned.sortedByCoord.out.bam -r gencode.v36.annotation.gene.bed Results in: This is PairEnd Data Fraction of reads failed to determine:…

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RSeQC confusing output – Half fails to determine, half is reverse strand

RSeQC confusing output – Half fails to determine, half is reverse strand 0 Hello, I am checking the strandness of a sample using infer_experiment.py and I got a pretty confusing result (for me). infer_experiment.py -i sample_Aligned.sortedByCoord.out.bam -r gencode.v36.annotation.gene.bed Results in: This is PairEnd Data Fraction of reads failed to determine:…

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How To Split Multiple Samples In Vcf File Generated By Gatk?

There now also is a plugin in bcftools which does the split in a single pass over the multi-sample VCF/BCF file. It does not seem to be very fast, but looks correct and there are options to do the split in custom ways. You do need to install bcftools with…

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README – DeepDeblur-PyTorch

2021-11-11 09:04:40  阅读:6  来源: 互联网 标签:— py dataset python PyTorch DeepDeblur README GPUs main This is a pytorch implementation of our research. Please refer to our CVPR 2017 paper for details: Deep Multi-scale Convolutional Neural Network for Dynamic Scene Deblurring[paper][supplementary][slide] If you find our work useful in your research or publication, please cite our work: @InProceedings{Nah_2017_CVPR, author…

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Cannot Move Kaggle.Json To /Root/.Kaggle In Colab

Navigate to www.kaggle.com. Then go to the Account tab of your user profile and select Create API Token. This will trigger the download of kaggle.json. Easiest way to download kaggle data in Google Colab 1. Go to your account Scroll to API section and Click Expire API Token to remove…

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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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XFEL Crystallography Postdoctoral Fellow

XFEL Crystallography Postdoctoral Fellow – 94193 Organization: MB-Molecular Biophys & Integ Bio Lawrence Berkeley National Lab’s (LBNL, www.lbl.gov/) Molecular Biophysics & Integrated Bioimaging Division has an opening for a XFEL Crystallography Postdoctoral Fellow to join the team. In this exciting role you will work as part of a group focusing…

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Why conda installs old pytorch with by default with cudatoolkit=11.2

I am trying to install conda for cudatoolkit=11.2 on google colab using: conda install pytorch cudatoolkit=11.2 -c pytorch -c nvidia But why does it install old pytorch=1.0.0 version not something >1.6? If I try to force install pytorch=1.6, it gives the following error: UnsatisfiableError: The following specifications were found to…

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Cross compiling dynamic parallelism for jetson aarch64 cuda 10.2 nvlink error – Jetson TX2

Hi, I have been trying to port dynamic parallelism to jetson aarch64 with cuda 10.2 installed. After having been suggested here to build the samples, I have tried and I am still getting this error: root@7f32bae9284e:/cuda-samples/Samples/cdpQuadtree# make TARGET_ARCH=aarch64 >>> GCC Version is greater or equal to 5.0.0 <<< /usr/local/cuda/bin/nvcc -ccbin…

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Fast way to extract specific sequences from large fasta

Fast way to extract specific sequences from large fasta 2 Hi all! I have ~2k text files, each with ~1k protein names (one protein name per line) and I need to extract the sequences of these proteins from a large master fasta file which contains ~5.5 million sequences. I wrote…

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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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How to find out which CpG sites constitute each DMR

Hi all, I know this is a late reply but i had the same issue so i wrote some code to help anyone who needs it in the future. It might be a bit crude but it works well! First take your final DMRcate output, mine was named “results.ranges” which…

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PRSice 2

PRSice 2 0 I am trying to calculate PRS in UKBB individuals for a binary trait (T2D). For that I am using the PRSice 2 software, This is how my code looks like, Rscript PRSice.R –prsice PRSice_linux –dir . –base base.BMI.adjn.txt –target T2test# –snp rsID –chr CHR –bp BP –A2…

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Bioinformatics Scientist II in Philadelphia, Pennsylvania

Location: LOC_ABRAMSON-Abramson Building  Req ID: 153191 Shift: Any Employment Status: Regular – Full Time  Job Summary The Bioinformatics Scientist II position is an entry level position for a PhD level professional and a 2nd stage position for those with moderate experience without a PhD. The focus of the position is service-level application of…

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ORF reading in Python

I am trying to read ORF from a list of sequences and identify the one with maximum length and correspond it to the sequence and the reading frame it belongs to as the output. I wrote the code and it’s not quite working properly. def startstop_codon(dna,frame): “”” TO CHECK THE…

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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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Research Associate at Imperial College London

Location: South Kensington Campus Job Summary  A bioinformatics research associate post with an emphasis on insect genomics is available in the research group of Dr. Nikolai Windbichler ((www.windbichlerlab.org/) working in collaboration with Dr. Angela Meccariello and Prof. George Christophides ((www.vigilab.org/) at Imperial College. Our joint research aims to build and…

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Transform a GTF file into a data frame in R

Transform a GTF file into a data frame in R 4 Hi, I would like to analyse the content of a GTF file. I am quite able with R and dplyr, so I would like to transform my GTF file into a data frame to facilitate my analysis. Does anybody…

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What is the best way to share an interactive Glimma glXY volcano plot with collaborators who do not work in R?

Hello, I have created an interactive volcano plot using the Glimma glXY function which creates a glimma-plots folder locally in my working directory, within which contains the html file for the volcano plot. The volcano plot is quite nice and I would like to share it with collaborators who do…

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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 to extract genes from goana

How to extract genes from goana 1 Hello, I am using goana to get enriched GO terms from my data. The problem I encounter is that I wish to find out what genes goana classes as ‘up’ or ‘down’ as the output from topGO() does not include this column. I…

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How to extract genes from goana

How to extract genes from goana 1 Hello, I am using goana to get enriched GO terms from my data. The problem I encounter is that I wish to find out what genes goana classes as ‘up’ or ‘down’ as the output from topGO() does not include this column. I…

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rank the usage of amino acids from fasta file using awk scripts

rank the usage of amino acids from fasta file using awk scripts 1 How can rank the usage of amino acids from fasta file using awk scripts? I am trying to write a awk script (rank.awk) which rank the usage of amino acids in fasta file. How can write the…

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Change CUDA Version in Colab or Kaggle – #2 by ptrblck – deployment

Hi, so i go to Start Locally | PyTorch and choose my system requirements i.e the following: Pytorch Build: Stable (1.10) Linux Pip Python CUDA Version: 11.3 The CUDA part can cause problems, as i run the following cmd on both kaggle and colab and get different CUDA version. Kaggle…

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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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Bioinformatics Research Associate – Job Opportunities

The core bioinformatics group at the Gurdon Institute, University of Cambridge is recruiting a bioinformatician to extend our capabilities in delivering world class research into developmental biology and cancer. This new group supports researchers across the institute in experimental design, analysis and presentation of high throughput data. Computational biology themes…

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Job Opening – Bioinformatics Analyst

job summary: As the world’s largest staffing and recruitment agency in the world, we can commit to find you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network…

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How to convert GEN or .gen format from impute.me to vcf on windows 10?

How to convert GEN or .gen format from impute.me to vcf on windows 10? 1 I tried for days to convert a gen file to vcf but it did not work. I am a beginner so i don’t know what are in vcf files and gen files or how they…

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sciClone input vaf file?

sciClone input vaf file? 3 Dear All, Hi, I want to use sciclone on our exome sequencing data. but one thing I can’t understand that is how can I got varCount equal to 0? I have no idea about this, following data i just grep from sciclone-meta-master manuscript figure3 data…

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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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implicit declaration of function ‘devm_ioremap_nocache’; did you mean ‘devm_ioremap_release’?

Date Sun, 7 Nov 2021 17:40:07 +0800 From kernel test robot <> Subject [dinguyen:socfpga-5.14_v1 2/121] arch/arm/mach-socfpga/fpga-dma.c:571:15: error: implicit declaration of function ‘devm_ioremap_nocache’; did you mean ‘devm_ioremap_release’? tree: git.kernel.org/pub/scm/linux/kernel/git/dinguyen/linux.git socfpga-5.14_v1head: cc7ba8d9b34b85acfbeefb77fa57c116c733c2c4commit: c20d1db912279c6f64211ade1e47b3e4c6eeb436 [2/121] FogBugz #172665: Sample driver for DMA transfer to FPGA soft IP (FIFO)config: arm-allyesconfig (attached as .config)compiler: arm-linux-gnueabi-gcc (GCC)…

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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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Leverage Azure NetApp for R Studio workloads

R is an open-source language used for statistical computing and graphics. It’s used in the statistical analysis of genetics, natural language processing, analysing financial data, and more. R provides an interactive command line experience. RStudio is an interactive development environment (IDE) available for the R language. The free version provides code editing tools, an integrated…

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Bioinformatics Scientist – Job at DAWSON in Bethesda, MD

Bioinformatics Scientist Full Time Prof-Entry Bethesda, MD, US DAWSON is a Native Hawaiian Organization 8(a) small business that brings the Spirit of Aloha to our employees. As part of the DAWSON “Ohana”, you will be provided a best-in-class benefits program that strives to ensure our great people have peace of…

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Installing ggplot “subscript out of bounds” error

Installing ggplot “subscript out of bounds” error $ R R version 2.12.2 (2011-02-25) Platform: i486-pc-linux-gnu (32-bit) > install.packages(“ggplot2″, dep=”T”) Error in apply(available[p1, dependencies, drop = FALSE], 1L, function(x) paste(x[!is.na(x)], : subscript out of bounds What can I do to install ggplot2? Answer #1: Do read the help for functions! From…

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Bioinformatics Programmer/Analyst – Job at RTI Research Triangle Institute in Washington, DC

The GenOmics, Bioinformatics, and Translational Research Center at RTI International has an opening for a Bioinformatics Programmer/Analyst interested in applying their computational and analytical skills within a team of researchers who leverage high-dimensional, multi-omic data sets to discover biomarkers of human health and disease. Who we are:Our team is a…

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Bioinformatics DevOps Engineer, remote at Quest Diagnostics in Alameda, California

Job Description: Look for more than answers. At Quest, we are on a continuous journey of discovery and development. It’s this attitude that has made us an industry leader and the #1 Diagnostic Lab in the US. For those joining us, we offer exciting and fast moving career opportunities where…

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Run AlphaFold v2.0 on Amazon EC2

After the article in Nature about the open-source of AlphaFold v2.0 on GitHub by DeepMind, many in the scientific and research community have wanted to try out DeepMind’s AlphaFold implementation firsthand. With compute resources through Amazon Elastic Compute Cloud (Amazon EC2) with Nvidia GPU, you can quickly get AlphaFold running…

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Splitting A Vcf File

Splitting A Vcf File 7 Hi i downloaded a VCF file conatins multiple genome data(Muliple sample)> i want to split the VCF file to each geome file(VCF file with 1 geome). I diidnt find any script. if you have any please share with me vcf • 18k views I know…

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Splice sequence indexing failed with err =127

Tophat2 Error: Splice sequence indexing failed with err =127 0 I’ve been trying to map my RNA-seq results onto an entire genome, and I’ve encountered a problem with splices. The script.pbs I submitted to cluster servers is: #PBS -N tophat_cufflinks_1 #PBS -o tophat_cufflinks_1_out.txt #PBS -e tophat_cufflinks_1_error_out.txt #PBS -l nodes=cu01:ppn=24 export…

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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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Eliassen Group hiring Java Architect / REST, SOAP, OpenAPI in Franklin, Massachusetts, United States

Job Description**100% REMOTE – Qualified applicants must be willing to work EST hours.** We’re looking for a highly skilled and experienced Java Architect to influence, educate, and enable custom connector developers to achieve successful outcomes. Due to client requirement, applicants must be willing and able to work on a w2…

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Java Architect / REST, SOAP, OpenAPI in Franklin, MA at Eliassen Group

**100% REMOTE – Qualified applicants must be willing to work EST hours.** We’re looking for a highly skilled and experienced Java Architect to influence, educate, and enable custom connector developers to achieve successful outcomes. Due to client requirement, applicants must be willing and able to work on a w2 basis….

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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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Synectics Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Contract: 3 months Pay: $22.91/hr ONSITE Description Perform bulk differential gene (ideally microarray and RNA-seq) and enrichment analysis in the R programming language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene (limma/varianceParition dream or other R method) and single-sample…

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connectwidgets – RStudio Documentation

Authored By Ashley Henry – Technical Writer When you want to share deployed content as a cohesive project How do you make sure your audience finds what they need on RStudio Connect without having to page through the dashboard, remember the right search terms, or bookmark every content item you…

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Spectraforce Technologies hiring Bioinformatics analyst in Waukegan, Illinois, United States

Job Title: Bioinformatics analystLocation: Lake County, IL; 100% remoteDuration: 6 months Payrate: $24/hr on W2 DescriptionWe have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or…

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gromacs 2021.4 – Download, Browsing & More

gromacs 2021.4 – Download, Browsing & More | Fossies Archive “Fossies” – the Fresh Open Source Software Archive Contents of gromacs-2021.4.tar.gz (5 Nov 09:47, 38023262 Bytes) About: GROMACS performs molecular dynamics, i.e. simulates the Newtonian equations of motion for systems with hundreds to millions of particles (designed for biochemical molecules…

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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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How To Configure Rstudio Package Build To Work Across Multiple Machines

Another common scenario is to setup two repositories in RStudio Package Manager one to serve CRAN packages and one to serve internal packages. This setup also. You can edit and save these scripts using a text editor. The material in this book was developed using the interactive integrated development environment…

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Re: [PATCH] net: uclass: Save ethernet MAC address when generated

Re: [PATCH] net: uclass: Save ethernet MAC address when generated – Michael Walle From: Michael Walle <michael@walle.cc> To: rfried.dev@gmail.com Cc: git@xilinx.com, joe.hershberger@ni.com, michal.simek@xilinx.com, sjg@chromium.org, u-boot@lists.denx.de, Michael Walle <michael@walle.cc> Subject: Re: [PATCH] net: uclass: Save ethernet MAC address when generated Date: Tue, 2 Nov 2021 10:00:15 +0100 [thread overview] Message-ID: <20211102090015.2395446-1-michael@walle.cc>…

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Looking for a faster way to get doi of pubmed publications

Is there a faster way to get pubmed doi using an input list of PMIDs? Alternatively is there a way to do all of this in R Bioconductor? import metapub from Bio import Entrez, Medline # Function to get the number of publications matching a query term def pubmed_publications_count(term): Entrez.email…

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Failed to create symbolic link. Trinity

Failed to create symbolic link. Trinity 0 This error appears if my output file is at /mnt/…(drive). But if an output file is in home directory – trinity runs well And some strange situation, when I wrote *sudo” the program cannot find salmon, but without this one, it runs well….

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Covariate correction which data take for downstream analysis?

Hi, I am really bad in stats so I am really sorry if this question is inappropriate or too stupid (also I wasn`t if this was the right forum…if not, apologies again!). A collaborator asked me to correct for age and sex using linear regression) our bulk-RNAseq dataset (6 human…

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Dir, Bioinfo & Comp Biology

Dir, Bioinfo & Comp Biology Back Apply Share Requisition no: 520104 Work type: Full Time Location: Medical Center School/Department: Center for Infection and Immunity Grade: Grade 106 Categories: Research (Lab and Non-Lab) Job Type: Officer of…

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Cherokee Federal hiring Bioinformatics Associate in Silver Spring, Maryland, United States

Job DescriptionJoin the team who values your skills and expertise. Cherokee Nation Technology Solutions (CNTS) supports federal clients with a full life-cycle approach to military medical health and research programs. CNTS uses a personalized program management methodology to solving clients’ toughest challenges, helping you make the most of your skills….

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How to append two fastq files ?

How to append two fastq files ? 1 Dear Biostars, How can I append sequences of two fastq files ? Suppose we have two fastq files: **file1.fastq** @HEADER CTCAGNTTGG + AAAAA#EEEE @HEADER GTGAGTTTAG + AA<AA#EE<E **file2.fastq** @HEADER CTTTA + #EEEA @HEADER GTGAG + A#E<E **result.fastq = append file2.fastq to file1.fastq**…

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Calculate allele frequency from many VCF files in specific locus

Calculate allele frequency from many VCF files in specific locus 1 Dear all, I have 100 VCF files (100 different samples). I would like to calculate allele frequency in specific sites. In one specific locus I have three genotypes (GATK best practices workflow): rs-xxxxx: A/A occurring in 30 samples (ref…

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

Located in Boston and the surrounding communities, Dana-Farber Cancer Institute (DFCI) brings together world renowned clinicians, innovative researchers and dedicated professionals, allies in the common mission of conquering cancer, HIV/AIDS and related diseases. Combining extremely talented people with the best technologies in a genuinely positive environment, we provide compassionate and…

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Field Bioinformatics Scientist – Olympia

When you’re part of the team at Thermo Fisher Scientific, you’ll do important work, like helping customers in finding cures for cancer, protecting the environment, or making sure our food is safe. Your work will have real-world impact, and you’ll be supported in achieving your career goals. **How will you…

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Bioinformatics Analyst position in North Chicago, Illinois

Open for discussion of Remote  We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene?ideally microarray and RNA-seq) and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential…

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Converting Bam To Bedgraph For Viewing On Ucsc?

Perhaps try BEDOPS bam2bed and sort-bed to convert your BAM data to UCSC BED? $ bam2bed < foo.bam | sort-bed – | cut -f1-6 > foo.bed Then make a custom track from it, using the full, pack or squish display modes. If you zoom out far enough, you can get…

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DESeq2 MA plot label subset of genes

DESeq2 MA plot label subset of genes 2 Hello, I’m new to R and I’m trying to make a MA plot from my DESeq2 results using ggplot2. I have figured out how to make a MA plot using the following code: plot_poly <- all_counts.poly.results %>% as.data.frame() %>% ggplot(aes(log2(baseMean), log2FoldChange) +…

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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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Trouble installing Bioconductor packages inside a conda environment.

I would appreciate some assistance resolving Bioconductor R package installation problems within a conda environment. I have an Ubuntu machine with three accounts: root, user 1 with sudo privileges and part of group 1001, and user 2 also part of group 1001. This machine has a fresh installation of Ubuntu,…

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Generating heatmaps of pre-selected candidate genes after deseq2

Generating heatmaps of pre-selected candidate genes after deseq2 2 Hi biostars, Is it possible to make a heatmap for a preselected list of genes after deseq2 DGE analysis? I wanted to represent the log2FC of 20 differentially expressed candidate genes as a heatmap. RNA-Seq DESEq2 heatmap • 4.1k views Hi,…

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Select a list of genes of interest to visualise in heatmap of DESeq object

Select a list of genes of interest to visualise in heatmap of DESeq object 1 Hi, I have previously generated heatmaps of the top x genes in DESeq2 using the following code: topVarGenes <- head(order(rowVars(assay(rld)), decreasing = TRUE), 20) mat <- assay(rld)[ topVarGenes, ] mat <- mat – rowMeans(mat) anno…

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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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Question about VCFtools –window-pi –window-pi-step

Hi all I’m using VCFtools (v0.1.17) for estimating nucleotide diversity of my study species. I already got a VCF file which was made form mapping to a draft genome, then I used it to calculate pi value. As you can see, the output showed the bin size and variants(here, I…

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Research Engineer in Bioinformatics / System development

KTH Royal Institute of Technology in Stockholm has grown to become one of Europe’s leading technical and engineering universities, as well as a key centre of intellectual talent and innovation. We are Sweden’s largest technical research and learning institution and home to students, researchers and faculty from around the world….

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Bioinformatics Scientist – Job at University of North Carolina

Primary Purpose of Organizational Unit The UNC School of Medicine has a rich tradition of excellence and care. Our mission is to improve the health and wellbeing of North Carolinians, and others whom we serve. We accomplish this by providing leadership and excellence in the interrelated areas of patient care,…

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Bioinformatics Programmer – architect / engineer / cad

QR Code Link to This Post MilliporeSigma is hiring a Bioinformatics Programmer at their Rockville, MD location A career with MilliporeSigma is an ongoing journey of discovery: our 58,000 people are shaping how the world lives, works and plays through next generation advancements in Healthcare, Life Science and Electronics. For more…

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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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DESeq2 ratio of ratios and p-value

Hello, I am new to DeSeq2 and I am trying to use a multi-factor design to answer this question: Is captured/input in condition 1 different from captured/input in condition 2 ? I used a combination of the DeSeq2 manual and DESeq2 testing ratio of ratios (RIP-Seq, CLIP-Seq, ribosomal profiling) to…

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Bioinformatics Specialist I – Center for Genomic Medicine

GENERAL SUMMARY/ OVERVIEW STATEMENT: The Talkowski Laboratory in the Center for Genomic Medicine at Massachusetts General Hospital (MGH) is seeking a motivated, enthusiastic candidate to join our research group. Bioinformatics Specialist I advances computational component of biomedical research at the department and throughout the hospital. Works closely with other investigators…

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FASTAFS: file system virtualisation of random access compressed FASTA files | BMC Bioinformatics

FASTA File System (FASTAFS) file format consists of four blocks: (1) File Header (2) Per-Sequence-Data (3) Per-Sequence-Header and (4) File Metadata, to efficiently store sequence and metadata (Fig. 1). During conversion, the metadata flag sets the archives status to incomplete. Each block of compressed sequence data is followed by the CRAM…

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Bioinformatics Programmer – software / qa / dba / etc

QR Code Link to This Post MilliporeSigma is hiring a Bioinformatics Programmer at their Rockville, MD location A career with MilliporeSigma is an ongoing journey of discovery: our 58,000 people are shaping how the world lives, works and plays through next generation advancements in Healthcare, Life Science and Electronics. For more…

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