Open Source Biology & Genetics Interest Group

Mitochondria.Credits: Wikipedia Commons One of the first population-scale studies on how common genetic traits are affected by changes in mitochondrial DNA, the driving force of human cells, was the European Molecular Biology Laboratory at the Wellcome Trust Sanger Institute, University of Cambridge, EMBL. Tokoro (EMBL-EBI) and its collaborators. The team…

News:fastp 0.22 released, with new FASTQ deduplication feature. 0 fastp is a fast all-in-one preprocessing tool for FASTQ data. Now a new version v0.22.0 has been released, with a FASTQ deduplication feature. Specify -D or –dedup to enable this option. fastp • 16 views • link 2 hours ago by…

WASHINGTON, D.C. (Release) – The Defense POW/MIA Accounting Agency (DPAA) announced today that Marine Corps Reserve Pfc. Jack E. Hill, 21, of Casper, Wyoming, killed during World War II, was accounted for on June 26, 2020. In November 1943, Hill was a member of Company D, 1st Battalion, 6th Marine…

From idat Illumina Infinium MethylationEPIC to CNV analysis for homo/hetero-zigous deletion 0 Hi, My group works on cancer and we have difficulty on a little part of our last project about malignant pleuric mesothelioma. I’m looking for help in the analysis of .idat from genome-wide DNA methylation profiles obtained via…

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…

Postdoctoral researcher Microbiome Bioinformatics 100%, Zurich, fixed-term 100%, Zurich, fixed-term The Food Systems Biotechnology (FSB) group is seeking a postdoctoral researcher with expertise in microbiome metagenomics and bioinformatics to lead efforts for characterization and analysis of global microbial biodiversity as part of the Microbiota Vault initiative’s efforts to preserve our microbial…

Post Jobs 2 jobs   Get new jobs for this search emailed to you: Sequence Bioinformatics Inc. St. John’s NL Research Assistant Sequence Bio is a passionate Newfoundland and Labrador company striving to change the future of healthcare right here at home. But, we need your help! We are looking for……

You will have: • B.S./M.S. in Computer Science or Bioinformatics, with 2-4 years of related professional experience• Domain knowledge in bioinformatics and experience in working with omics data• Experience with a combination of Python, R• Experience working in Linux environment and proven knowledge of Linux command line utilities• Experience with…

Leukocare AG is a fast growing, international biotech company located in Martinsried/ Munich, Germany and Milford, MA, USA. Based on our technology platform, we develop superior and innovative drug product formulations combining state-of-the-art analytical technologies with innovative bioinformatics approaches. Together with our partners within Pharma, Biotech and the Medical Devices…

Job Summary Primary accountability is to leverage the organization’s data assets exome sequencing data (>180,000 individuals) from MyCode Community Health Initiative to improve quality, efficiency and generate knowledge specifically in the field of bioinformatics within health research. Performs and supervises complex data extraction, transformation, visualization, and summarization to support Research…

Bioinformatician/Molecular Biologist Grade: HSO New Haw The Animal and Plant Health Agency (APHA) is an executive agency of the Department for Environment, Food & Rural Affairs, and works on behalf of the Scottish Government and Welsh Government. Our diverse teams of over 2,000 skilled and committed professionals come together to…

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…

About us Champions Oncology is a technology-enabled research organization that leverages an end-to-end range of research and development solutions to improve the productivity of oncology drug development. Using computational and experimental testing platforms, Champions Oncology improves decision making for effective therapeutic development. Our team is passionate and self-motivated working together…

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

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…

How to align and visualize data with .fasta and .gff3 files in IGV? 1 Hi everyone, I have an issue in aligning and visualizing my data in IGV. As I read in manual of IGV, to align and visualize data, I need to to prepare .BAM/.SAM or other input format…

Forum:What are some of the problems faced by bioinformaticians because the wet lab personell couldn’t understand how data analysis was done? 0 Many wetlab personel have little to no idea on the problems faced by bioinformaticians when it comes to designing the experiment, for example in RNA-Seq data analysis, we…

I want to change the color of text by file type in PuTTY 1 Hello To use ubuntu terminal in my laptop, I use application PuTTY. Unlike ubuntu terminal, the PuTTY always shows only white text regardless of the file format. But on the screens of other users show different…

Bowtie2 hg19 reference for gatk MuTect 3 Hello, I understand that the suggested aligner to use with GATK is bwa. If I want to use Bowtie2 as the aligner, which reference file should I be using? The reference in GATK bundle (Homo_sapiens_assembly19.fasta) does not seem to work with Bowtie2 and…

Lake trout is an iconic native species to the Great Lakes. An MSU doctoral student is leading an effort along with his professor and an international team of researchers from the U.S. and Canada spearheaded by Louis Bernatchez at Université Laval to create a reference genome for lake trout to…

For context: I’m using macOS Big Sur and have successfully run AutoDock Vina through my terminal, after which I’ll view the output in ChimeraX. Also, I’m an undergrad attempting to teach myself how to use docking software for a personal project and future use, so I may very well have…

SAN CRISTOBAL ISLAND, Galapagos (AP) — An innovative project in the remote Galapagos islands has turned dozens of local inhabitants into citizen scientists at a moment when the pandemic has dried up tourist income. The participants have been hired and trained to sample the genetic diversity in the small island…

Delphi property AutoDock: Boolean read FAutoDock write FAutoDock default 1; C++ __property AutoDock = {default=1}; Properties Description Determines whether the control bar temporarily docks drag clients to provide visual feedback. Vcl.ExtCtrls.TControlBar.AutoDock inherits from Vcl.ExtCtrls.TCustomControlBar.AutoDock. All content below this line refers to Vcl.ExtCtrls.TCustomControlBar.AutoDock. Determines whether the control bar temporarily docks drag…

Extraction and detection of single-molecule DNA from cells using 3D integrated nanopores. Credit: Makusu Tsutsui et al. The ability to detect DNA from a single cell is important for the detection of diseases and hereditary diseases. Measurement of a single DNA molecule has long been possible. However, the sample cannot…

Editor’s Note: Some of the articles described below are not yet available at the PNAS site, but they are scheduled to be posted this week. An international team tallies genetic variation and population structure in present-day Turkey, using a combination of exome and whole-genome sequencing. Based on exome sequences for…

Hi Stars, I would appreciate it if you share your inputs on the following issue: I am trying to make binary classifier models to classify variants into tow diffrent classes. The dataset is an annotated variant file with dimensions as 187,643 x 203. The first column contains class labels with…

. 2021 Aug 13;142:107927. doi: 10.1016/j.bioelechem.2021.107927. Online ahead of print. Affiliations Expand Affiliations 1 Biophysical Research Group, Faculty of Natural Sciences, Vytautas Magnus University, Vileikos st. 8, LT 44404 Kaunas, Lithuania. 2 Departament of Bioelectronics, Mines Saint-Etienne, 880 route de Mimet, Gardanne 13541, France. 3 Biophysical Research Group, Faculty of…

Association test to get p values and OR in plink2, and file input format? 0 Are there any commands for association testing in plink2 which will output p-value and OR in the resulting output file? If so, what kind of file input do I need to use for such commands?…

Tsuneaki Kenzaka,1,2 Yuto Shinkura,1 Shizuo Kayama,3– 5 Liansheng Yu,3– 5 Sayoko Kawakami,3 Motoyuki Sugai,3– 5 Satoru Kawasaki1 1Department of Internal Medicine, Hyogo Prefectural Tamba Medical Center, Tanba, Japan; 2Division of Community Medicine and Career Development, Kobe University Graduate School of Medicine, Kobe, Japan; 3Antimicrobial Resistance Research Center, National Institute of…

Il mercato del Military Tank Container dovrebbe crescere a un CAGR di circa nei prossimi cinque anni, raggiungerà milioni di dollari nel 2024, dai milioni di dollari nel 2021, secondo un nuovo studio. Il rapporto Military Tank Container fornisce tendenze di crescita, con varie parti interessate come investitori, amministratori delegati,…

Accounting Assistant EMBL – European Molecular Biology Laboratory Heidelberg, Germany Organisation data: FinanceJob number: HD02047Contract Type: Staff MemberJob Function: Administrative Assistant (gr. 3-4)Closing date: 20 September 2021 About the team/job We are Europe’s flagship research laboratory for the life sciences – an intergovernmental organisation performing scientific research in disciplines including…

Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…

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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INTRODUCTION Clustered regularly interspaced short palindromic repeats (CRISPR) are a family of DNA sequences, which constitute a primitive immune system that is responsible for protecting prokaryotic cells from phage infections. New York, Aug. 24, 2021 (GLOBE NEWSWIRE) — Reportlinker.com announces the release of the report “CRISPR Based Therapeutics Market by…

About the team/job We are seeking a HPC engineer to join our Compute team within our Technical Services Cluster (TSC), serving an institute of over 800 researchers and technical staff. You will be working closely with members of the department, and more widely with technical users across EMBL-EBI, playing an…

Dante vs Nebula indexcov 0 I’m trying to understand the variance of the same individual on the same chromosomes tested on Dante 30x and Nebula 100x. Is this expected? Other chromosomes are not as drastic. Which WGS is more “the truth” ? dante nebula indexcov • 27 views Login before…

Significance Many animals depend on maternally transmitted symbiotic bacteria that provide nutrients or other benefits. The evolution of these symbionts is complicated: natural selection can act on hosts, favoring symbionts that increase host reproduction, or on symbionts, favoring symbionts that spread within hosts. Furthermore, transmission bottlenecks can facilitate the spread…

Bwa sampe error 999 25-08-2021 I’m getting the following error message when I try to import into 1aa.vremenagoda54.ru file (using samtools import). [samopen] SAM header I’m using bwa aln to find coordinates and bwa sampe to…

Shear simulation lammps error 25-08-2021 I am trying to calculate shear-stress vs shear strain in Graphene. I made two group of atoms upper and lower, out of which for upper, I setforce 0, 0, 0 and for…

Min. Order 1 Set Trade Assurance protects your orders Multiple safe payment options Worry-free shipping & quality Build your credibility Place of Origin: Guangdong China Brand Name: GLM Model Number: H-031 Whitening Injection Machine Certification: ce Feature: Skin Rejuvenation, Detox Material: ABS & Stainless Steel Waterproof: NO Warranty: 1 Year…

A building on the Illumina Campus in University City. Reuters/Mike Blake The U.S. Federal Trade Commission on Tuesday said it seeks to unwind life science company Illumina‘s $7.1 billion acquisition of Grail, alleging it would harm innovation and boost prices. FTC senior counsel Susan Musser said in her opening statement…

Ask questionssamtools sort not working Hi There, I just found a new issue: samtools sort output is not sorted. Seems it did not do anything. The content is still the same as the unsorted bam or sam files. Here is how I tested it: Upload a sam file 2.sam; samtools…

How get Genetic Positions of SNPs? 0 I have some datasets related to different diseases like AML, etc. The data which I have include markers’ genotypes (AA, AB, BB) and some other information like chromosome number, physical position, strand,etc. For some reasons I need to have the genetic positions of…

The gap between two doses of coronavirus vaccine Covishield may be reduced. The suggestion to reduce the gap has been given by IAPSM i.e. Indian Association of Preventive and Social Medicine, an organization working in the health sector. In this regard, IAPSM says that the central government is considering the…

(Reuters) – The U.S. Federal Trade Commission on Tuesday said it seeks to unwind life science company Illumina Inc’s $7.1 billion acquisition of Grail Inc, alleging it would harm innovation and boost prices. FTC senior counsel Susan Musser said in her opening statement at a trial in Washington that cancer…

Latest version of com.github.samtools:htsjdk javadoc.io/doc/com.github.samtools/htsjdk Current version 1.133 javadoc.io/doc/com.github.samtools/htsjdk/1.133 package-list path (used for javadoc generation -link option) javadoc.io/doc/com.github.samtools/htsjdk/1.133/package-list Read more here: Source link

DOI: 10.18129/B9.bioc.unifiedWMWqPCR     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see unifiedWMWqPCR. Unified Wilcoxon-Mann Whitney Test for testing differential expression in qPCR data Bioconductor version: 3.11 This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing…

Getting Started With Kaggle #1: Text Data (Quora Question Pairs, Spam SMSes) | Jessica Yung Exciting Kaggle Competitions With Cash Prizes In Data Science Kaggle Text Data Dating lofconf.ristoranteallacacciatora.it 24.8.2021 If you are a data science professional or a machine learning…

“We want to promote a better kind of strawberry in Singapore,” says Dr. Shengjie Bao, director and co-founder of Singrow Pte Ltd., a Singaporean agtech company specializing in indoor production of strawberries, cherry tomatoes and other products. Shengjie and his co-founder Xu Tao founded Singrow Pte Ltd. to facilitate the…

Full Digital Access + 7 Day Delivery costs $25 billed approximately monthly for the first 3 months. After the first 3 months, the cost is $65 billed approximately monthly. Renewals occur automatically unless cancelled in accordance with the full Terms and Conditions. Each payment, once made, is non-refundable, subject to…

As the Head of Reagent Bioinformatics in the Molecular Lab Applications chapter you will play a key role in advancing Roche’s class leading portfolio of sequencing reagents across sample preparation, library preparation, and target enrichment. Working in close partnership with wet lab, software, and commercial colleagues, you will build a…

With a handful of drugs for cystic fibrosis already approved, Vertex Pharmaceuticals has turned its attention to expanding its pipeline through collaborations and acquisitions the past few years. Today, the California company announced a new agreement with an old partner. Nearly three years ago, Vertex and Arbor Biotechnologies struck a deal….

doi: 10.1096/fj.202100873RR. Bradley A Ruple  1 , Joshua S Godwin  1 , Paulo H C Mesquita  1 , Shelby C Osburn  1 , Christopher G Vann  1 , Donald A Lamb  2 , Casey L Sexton  1 , Darren G Candow  3 , Scott C Forbes  4 , Andrew D Frugé  2 , Andreas N Kavazis  1 , Kaelin C Young …

Carnivorous plants of utricularia janarthanamii species of bladderwort family that prey on insects have been found in the hilly Girnar forest near Junagadh city, according to a team of researchers of the Department of Life Sciences of the Bhakta Kavi Narsinh Mehta University (BKNMU), Junagadh. The presence of these plants…

In the final, hectic days of a recent Kaggle competition I found myself in want of more GPU power. As one often does in such an occasion. My own laptop, with its GPU setup, was doing a fine job with various small models and small images, but scaling up both…

How I do lift over a Plink bim file from Hg18 to Hg19. 2 I’ve got some very old SNP data from Data Dryad. The BIM files uses coordinates from Hg18, but my dataset uses coordinates from Hg19. I was wondering if anyone knows how to liftover coordinates in a…

Entry C00511                      Compound                                Name Acrylic acid;Propenoate;Acrylate;2-Propenoic acid;Vinylformic acid Formula C3H4O2 Exact mass 72.0211 Mol weight 72.0627 Structure Mol fileKCF fileDB search Reaction Pathway map01120   Microbial metabolism in diverse environments map01220   Degradation of aromatic compounds Enzyme Other DBs KCF data Show ATOM        5            1   C6a C    25.5500  -16.7300            2   C2b C    26.7400  -17.4300            3   O6a O    25.5500  -15.3300            4   O6a O    24.3600  -17.4300            5   C2a C    28.0000  -16.7300BOND        4            1     1   2 1            2     1   3 1            3     1   4 2            4     2   5 2 Read…

DOI: 10.18129/B9.bioc.MeSH.Pto.eg.db     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see MeSH.Pto.eg.db. Mapping table for Pan troglodytes Gene ID to MeSH Bioconductor version: 3.11 Entrez Gene ID to MeSH ID table. Author: Itoshi NIKAIDO, Koki Tsuyuzaki, Gota Morota, Takeru Nakazato Maintainer: Koki…

Vcf file sorting 1 I got vcf file from my instructor. It is VEP annoted with over 50 options separated by ||. I noticed that the vcf is not arrange to appropriate columns so I decided to sort it. I used this code to sort my vcf file according position:…

KEGG COMPOUND: C04751     COMPOUND: C04751 Help Entry C04751                      Compound                                Name 1-(5-Phospho-D-ribosyl)-5-amino-4-imidazolecarboxylate;1-(5′-Phosphoribosyl)-5-amino-4-imidazolecarboxylate;1-(5′-Phosphoribosyl)-5-amino-4-carboxyimidazole;5′-Phosphoribosyl-5-amino-4-imidazolecarboxylate;1-(5′-Phosphoribosyl)-4-carboxy-5-aminoimidazole;5′-Phosphoribosyl-4-carboxy-5-aminoimidazole;5-Amino-1-(5-phospho-D-ribosyl)imidazole-4-carboxylate Formula C9H14N3O9P Exact mass 339.0468 Mol weight 339.1959 Structure Mol fileKCF fileDB search Reaction Pathway map01110   Biosynthesis of secondary metabolites Module M00048   Inosine monophosphate biosynthesis, PRPP + glutamine => IMP Enzyme Other DBs KCF data Show ATOM        22            1   N4y N    19.7356  -16.9708            2   C1y C    18.7758  -18.1993            3   C8y…

DOI: 10.18129/B9.bioc.cageminer     This is the development version of cageminer; to use it, please install the devel version of Bioconductor. Candidate Gene Miner Bioconductor version: Development (3.14) This package aims to integrate GWAS-derived SNPs and coexpression networks to mine candidate genes associated with a particular phenotype. For that, users…

VEP plugin uses 0 It is a small question, I downloaded all plugins and wrote in the input script to get plugin experimental functionalities (I am using merged cache Ref_Seq & Ensembl both). # make a file with a single variant using bash echo “17 43071077 43071077 T/C + variant_1″…

Psyt 502 error 25-08-2021 PSYT Issues in Drug Dependence 3 Credits PSYT Brain Evolution & Psychiatry 3 Credits PSYT Advanced Studies in Addiction 3 Credits. Syntax Error. Usage: dbname:identifier. KEGG, ENZYME: , Help. Entry. EC Enzyme….

DOI: 10.18129/B9.bioc.Single.mTEC.Transcriptomes     This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see Single.mTEC.Transcriptomes. Single Cell Transcriptome Data and Analysis of Mouse mTEC cells Bioconductor version: 3.8 This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data…

Sum of rows for GSEA analysis 0 Hi, I have an issue which looks like easy to solve, but I’m stuck. I have a dataframe composed of columns (significant pathways retrieved from GSEA) and rows (entrez gene ids). In this data frame there are 1 if a gene is present…

Showing : genbankr • reset updated 8 months ago by Nicholas • 0 • written 8 months ago by heiko_kin ▴ 50 9 results • Page 1 of 1 Traffic: 479 users visited in the last hour Read more here: Source link

pre-proccessing of RNAseq data for WGCNA 0 Hi everyone, i wanted to create an expression matrix for WGCNA input. however, i has been said that use RPKM/FPKM data instead of CPM, how can i change my TCGA data to RPKM/FPKM in GDCquery and how to filter expression set of genes…

Job Description Interim Bioinformatics Senior Analyst -Remote Working Pay Rate: Up to £600 per day pay range subject to IR35 status This role is currently remote working. Key Accountabilities: To report to the Bioinformatics lead and lead a Team of Bioinformatics Analysts To be responsible for outcomes in this policy…

Loading Virus Pathogen Database and Analysis Resource (ViPR)… Release Date: Jun 25, 2021 This system is provided for authorized users only. Anyone using this system expressly consents to monitoring while using the system. Improper use of this system may be referred to law enforcement officials.This project is funded by the…

Job Description6,000 people dedicated to discovery – 6 research campuses across the globe – 1 purpose…to reimagine medicine! Novartis Institutes for BioMedical Research (NIBR) 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…

Positional restraint energy is too big 0 Hello, I am running equilibration of protein system to prepare it for md simulation and I encountered a problem that says “Compute_Energy_Restraints_Pos> Positional restraint energy is too big (see “Chapter: Trouble shooting” in the user manual) rank_no = 15″. My system consist of…

##Genome-Annotation-Data-START## Annotation Provider::NCBI Annotation Date::08/10/2016 16:40:10 Annotation Pipeline::NCBI Prokaryotic Genome Annotation Pipeline Annotation Method::Best-placed reference protein set; GeneMarkS+ Annotation Software revision::3.3 Features Annotated::Gene; CDS; rRNA; tRNA; ncRNA; repeat_region Genes (total)::3,675 CDS (total)::3,608 Genes (coding)::3,557 CDS (coding)::3,557 Genes (RNA)::67 rRNAs::2, 1, 1 (5S, 16S, 23S) complete rRNAs::1, 1, 1 (5S, 16S,…

Corteva AgriScience, the agriculture division of DowDuPont, is the only major agri-science company completely dedicated to agriculture. By combining the strengths of DuPont Pioneer, DuPont Crop Protection, and Dow AgroSciences, we’ve harnessed agriculture’s brightest minds and expertise gained over two centuries of scientific achievement. Selected intern’s day-to-day responsibilities include: 1….

Hi, I am using WGCNA to construct a network and find significant genes for a trait of interest. After making the network, I chose a module based on the pvalue and correlation value. Then I calculated gene significance values for all genes in that module. trait_x <- as.data.frame(datTraits[, “trait_x”, drop…

how to use old and new smallRNAseq data sets for data analysis 0 I have some smallRNAseq data (already sequenced) and would like to generate smallRNAseq from another few samples. but at the end I would like to include both new and old batches in the data analysis. For smallRNA…

Dnasp Tutorial For Beginner 1 Hi Can someone help me? I need to know which data is required to perform different test with DNAsp: intra or interspecies sequences thank you • 6.1k views The “sp” in DNAsp stands for “sequence polymorphism” which reflects that this software is principally designed for…

miRNAseq analysis not shown adapter sequence and huge N’s content 0 Hi there, This is my third time doing miRNA sequencing analysis, so i do not have huge experience on this… So, i have 18 human semen samples, (also no experience in this type samples) i have been reading alot…

Mapping unique GO term description given a specific GO id 0 I have a list of GO ids and I want to find unique term description such that if I provide say 200 GO IDs I will give 200 specific GO terms. The code snippet I am using is given…

R vegdist does not compute distances for all my sites 0 I’m trying to create some MDS plots for my data. I’m using vegan package’s vegdist which does not produce any errors but when I view my resulting matrix there are empty values everywhere in the lower diagonal where only…

WNN (Seurat v4) vs. totalVI (scvi-tools) for CITE-seq data 0 I want to build a UMAP from CITE-seq data with a joint embedding of the scRNA-seq and protein ab data. What’s the ‘best’ method in terms of representing the most accurate embedding? In the totalVI paper, they say totalVI >…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sun, 22 Aug 2021 21:56:28 +0200 Source: python-biopython Architecture: source Version: 1.78+dfsg-5 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 986410 Changes: python-biopython (1.78+dfsg-5) unstable; urgency=medium . * d/control: update uploader address * d/watch:…

Package: routine-update Version: 0.0.6 Severity: important Hi Andreas, when working on making sure the python-biopython watch file was appropriately fixed, I saw routine-update choke with the following error: $ routine-update gbp:info: Fetching from default remote for each branch gbp:info: Branch ‘master’ is already up to date. gbp:info: Branch ‘pristine-tar’ is already up to date. gbp:info: Branch…

Effect of unequal sample sizes on p-value 1 Hello, I have performed the following test to test if the two groups are different. the p-value is very small, and its probably because of the high sample size. I want to ask if having unequal sample sizes in the two groups…

Calculate the fraction of genome that is feature X 2 I am trying to calculate enrichment of Structural variant breakpoints and SNV locations in genomic features (exon, intron, 5’UTR…) in a non-human genome. To know whether a feature is over/underrepresented in a SV/SNV dataset, I first need to know the…

Problems with downloading fastq files from sra-toolkit 1 I have been trying to download the fastq files of a single cell RNA experiment from SRX8632237 with the following SRA runs : SRR12108143 SRR12108144 SRR12108145 SRR12108146 The runs show that it has 3 reads per spot (link). However, I am unable…

How to compute module completion ratio of KEGG modules from KO identifiers? (command line) 0 I was previously using KEGG-MAPLE to compute module completion ratios for metagenome assembled genomes. However, this tool was web only (very frustrating) and also it has been discontinued. Now I’m trying to do something similar…

Compare two gene lists that are generated by two methods 0 I want to compare two methods. Both methods try to predict cancer driver genes. Assume that we know the ground truth that there are M genes in total and N out of M genes are driver genes. The first…

Ensembl VEP Docker: cannot write to FASTA lockfile 0 Hello, I am trying to use the Ensembl VEP tool to annotate a database after liftover. For ease of use (or so I thought) I followed all the necessary steps decribed in the official documentation. I want to use local cache…

RNASEQ – Mapping to genome or Transcriptome 1 What are the advantages and disadvantages of mapping to genome or transcriptome? Is there a good quality transcriptome available for Macaca Mulata and human? The advantage of mapping to transcriptome is definitely the time, it takes more time to map reads to…

Pipeline version control system, pipeline storage 0 Hello! Please take a few minutes. Your answer to the question is important to me) Do you use a version control system for your pipelines? If so, which one? Where do you store your pipelines? pipeline git storage • 64 views • link…

Gene Expression Threshold 0 Hello, I am a high school student working on a research project identifying the expression of relevant human cancer related genes in populus trichocarpa. I would like to display the gene expression values I have using a heatmap, but I am unsure of how to determine…

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…

Exctracting amino acid substitutions 0 Good day, I’m trying to develop a pipeline to determine mutations which are responsible for amino acid changes in genes associated with antibiotic resistance. I have roughly 300 bacrtial isolates. My approach so far has not been fruitful, in short this is what i tried:…

Filter duplicate ID from PLINK file 0 Hi All, I am new to SNP-chip data analysis. I have been exploring some SNP-chip data using plink 1.9, while checking the Relatedness using KING, I am getting an error of duplicate ID. I was wondering if there is any method I can…

WGCNA for diferent stages (I-IV) 0 I wanted to share my issue with WGCNA. any help would be very valuable for me I wanted to know that for identifying modules related with Stage I to Stage IV, how can i binarize these stages into 0, 1, 2, 3, respectively? i…

Get gene sequence for oragnism using python 0 Hi , If i have the Genus & Species how can i use them in python code to get a gene sequence. For example: SpecCode: 64588 Genus: Aapticheilichthys Species: websteri How can i use these date to get “Cox1” sequence in python…

relationship between DE-genes and DE-trascripts in deseq2 1 Hello everybody, I ran a DE –RNAseq project by star-stringtie2- deseq2 pipline. The prepDE.py was used for generation of transcript matrix and gene matrix. Deseq2 were performed at both gene and transcript levels. At the gene level, 838 DE-genes were identified with…

Senior Research Scientist, BioInformaticsUnited States – California – Foster City Gilead Sciences, Inc. is a research-based bio-pharmaceutical company that discovers, develops and commercializes innovative medicines in areas of unmet medical need. With each new discovery and investigational drug candidate, we seek to improve the care of patients living with life-threatening…

The Bioinformatics group in the Research and Technical Development organization at Illumina is seeking a talented Software developer. Our team works closely with internal and external collaborators to develop computational methods to resolve important clinical problems. This position will involve working closely with a team of bioinformatic scientists to develop…