Tag: query

ARCH= -gencode arch=compute for NX: – Jetson Xavier NX

hi,i am working on jetson Xavier NX box,i updated to jetpack 5.0.1 and deepstream6.1 right now.before i setup ARCH= -gencode arch=compute 72 for NX to train some models.but i cmake another file yesterday it detected arch-gencode 75!so i am confuse right now, should i setup 72 or 75 for jetson…

Continue Reading ARCH= -gencode arch=compute for NX: – Jetson Xavier NX

Induzierte pluripotente Stammzellen (IPSCs) Marktanteil, Analyse der wichtigsten Wettbewerber, Prognose bis 2028

Der Induzierte pluripotente Stammzellen (IPSCs) Market“-Forschungsbericht umfasst umfassende Daten zu vorherrschenden Trends, Treibern, Wachstumschancen und Einschränkungen, die die marktverändernden Aspekte der globalen Industrie variieren können. Dieser Bericht bietet eine eingehende Analyse der Marktsegmentierung, die Produkte, Anwendungen und geografische Analysen enthält. Der globale Induzierte pluripotente Stammzellen (IPSCs)-Marktbericht bietet eine genaue Beobachtung…

Continue Reading Induzierte pluripotente Stammzellen (IPSCs) Marktanteil, Analyse der wichtigsten Wettbewerber, Prognose bis 2028

Ubuntu Manpage: bamfillquery – fill query sequences into BAM files

Provided by: biobambam2_2.0.179+ds-1_amd64 NAME bamfillquery – fill query sequences into BAM files SYNOPSIS bamfillquery [options] <in.bam queries.fasta >out.bam DESCRIPTION bamfillquery reads a SAM/BAM/CRAM file and a FastA file, copies the sequences found in the FastA file into the query sequence field of the SAM/BAM/CRAM file and writes the resulting data…

Continue Reading Ubuntu Manpage: bamfillquery – fill query sequences into BAM files

How To Download Geo Data? Update New

Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Images related to the topicBioinformatics 101 | How to download RNA-Seq data from NCBI GEO | Bioinformatics for beginners Bioinformatics…

Continue Reading How To Download Geo Data? Update New

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

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

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

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

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

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

React Query Codegen from OpenAPI

Rapini is a new tool that can generate custom React Query hooks using OpenAPI (Swagger) files. The Command Line Interface (CLI) tool will take a path to an Open API file and generate a package that includes react hooks, typescript types and axios http requests – and this package is…

Continue Reading React Query Codegen from OpenAPI

a strange pattern of repetitive summits

Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits 0 Hi! I am trying to plot DNA binding profiles of my ChIP-seq bw files using Deeptools plotProfile. I generated the matrix using the computeMatrix reference-point. I used some publicly available bed files as my regions of…

Continue Reading a strange pattern of repetitive summits

Metagenomic Sequencing Market Size And Forecast

New Jersey, United States – The Verified Market Reports released the latest competent intelligence market research report on the Metagenomic Sequencing Market, The report aims to provide a thorough and accurate analysis of the Metagenomic Sequencing market, taking into account market forecast, competitive intelligence, technical risks, innovations, and other pertinent data. Its…

Continue Reading Metagenomic Sequencing Market Size And Forecast

Detailed differences between sambamba and samtools

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

Continue Reading Detailed differences between sambamba and samtools

Computational Biology Software Market Worldwide Industry Share 2022-2028

“ The report studies the key segments in global Computational Biology Software industry, their growth in past few years, profiles and market sizes of individual segments, and gives a detailed overview of the profiles of various segments. The report also presents key products and various other products in the global…

Continue Reading Computational Biology Software Market Worldwide Industry Share 2022-2028

Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) – Global Variome shared LOVD

Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) Chromosome 10 Allele Unknown Affects function (as reported) Probably does not affect function Affects function (by curator) Not classified Classification method – Clinical classification likely benign DNA change (genomic) (Relative to hg19 / GRCh37) g.123278248A>G DNA change (hg38) g.121518734A>G Published as FGFR2(NM_022970.3):c.1035T>C (p.Y345=) ISCN – DB-ID FGFR2_000119 Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION record Segregation –…

Continue Reading Variant #0000255165 (NC_000010.10:g.123278248A>G, FGFR2(NM_000141.4):c.939+1245T>C) – Global Variome shared LOVD

Open API Market Size, Trends and Forecast to 2029

New Jersey, United States – The Open API Market report includes the upcoming challenges and opportunities in the market. It ensures a strengthened position in the market and a growing product portfolio by providing all the important details related to the market growth. It reveals some of the key insights and focuses…

Continue Reading Open API Market Size, Trends and Forecast to 2029

RPostgreSQL connections are expired as soon as they are initiated with doParallel clusterEvalQ

I was able to reproduce your problem locally. I am not entirely sure but I think the problem is related to the way clusterEvalQ works internally. For example, you say that dbGetQuery(con, “select inet_client_port()) gave you the client port output. If the query was actually evaluated/executed on the cluster nodes…

Continue Reading RPostgreSQL connections are expired as soon as they are initiated with doParallel clusterEvalQ

Database Administrator at European Molecular Biology Laboratory (EMBL)

About the team/job In this role you will join an established Database team of database administrators in order to support the ongoing database operations. The main duties for this post are: DBA of MySQL and MongoDB.The Database Team provides day-to-day Database Administration support , database performance tuning and query optimization…

Continue Reading Database Administrator at European Molecular Biology Laboratory (EMBL)

BlastX through Biopython

BlastX through Biopython 0 I have an unknown gene segment in the Human_gene.txt file and I want to run blastx (translated nucleotide) using the blast module of Biopython by making the E-value threshold 0.0001 and displaying the match result of 50 residues of query and subject. I am trying this…

Continue Reading BlastX through Biopython

Corporate Volunteering Platform Professional Market Records a Significant Growth by 2029

“ A comprehensive appraisal of the worldwide Corporate Volunteering Platform Professional market agglomerates basically engaged scientific outcomes and noteworthy data taking care of the vital necessities of the report peruses including market members across the worldwide Corporate Volunteering Platform Professional market, financial backers and business visionaries looking for profoundly conclusive…

Continue Reading Corporate Volunteering Platform Professional Market Records a Significant Growth by 2029

Bioinformatics Software Professional Market Records a Significant Growth by 2029

“ A comprehensive appraisal of the worldwide Bioinformatics Software Professional market agglomerates basically engaged scientific outcomes and noteworthy data taking care of the vital necessities of the report peruses including market members across the worldwide Bioinformatics Software Professional market, financial backers and business visionaries looking for profoundly conclusive examination result…

Continue Reading Bioinformatics Software Professional Market Records a Significant Growth by 2029

Senior Research Associate/Principal Research Associate, Bioinformatics job with Vedanta Biosciences

Title: Senior Research Associate/Principal Research Associate, Bioinformatics Location: Cambridge, MA, or up to 100% remote Reports to: Scientist I, Bioinformatics The Role: We are looking for a bioinformatician/computational biologist to support the Research and Development team in the maintenance and querying of an existing laboratory information management system (LIMS), construction…

Continue Reading Senior Research Associate/Principal Research Associate, Bioinformatics job with Vedanta Biosciences

Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Experimental design and processing steps For the EpiSCOPE study [20], DHA supplementation and gender were balanced as much as possible across the 12 450K BeadChips on each glass slide, with these factors also randomly distributed over the 6 rows and 2 columns of 31 slides (Additional file 1: Fig. S1). Blood…

Continue Reading Batch-effect detection, correction and characterisation in Illumina HumanMethylation450 and MethylationEPIC BeadChip array data | Clinical Epigenetics

Postdoctoral Research Fellow in Bioinformatics/Computational Biology

Details Posted: 27-Apr-22 Location: Boston, Massachusetts Salary: Open Categories: Staff/Administrative Internal Number: 2022-27118 Located in Boston and the surrounding communities, Dana-Farber Cancer Institute 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…

Continue Reading Postdoctoral Research Fellow in Bioinformatics/Computational Biology

NcbiblastpCommandline alignment results are different from blast webpage

What you are trying to do is fairly simple, and you are complicating it by: 1) not providing your sequences so that someone can reproduce your attempt; 2) giving a result in a form that is impossible to read. Be honest, can you make any sense of the result you…

Continue Reading NcbiblastpCommandline alignment results are different from blast webpage

R For SEO Part 3: Data Visualisation With GGPlot2 & Wordcloud

[This article was first published on R | Ben Johnston, and kindly contributed to R-bloggers]. (You can report issue about the content on this page here) Want to share your content on R-bloggers? click here if you have a blog, or here if you don’t. R For SEO Part 3:…

Continue Reading R For SEO Part 3: Data Visualisation With GGPlot2 & Wordcloud

Molecular Modeling Software for Chemistry Market Size, Scope And Forecast

New Jersey, United States – The Molecular Modeling Software for Chemistry Market report is the ultimate tool to help industries, companies, and organizations make informed decisions for business growth. With the help of the market tactics and strategies covered here, it becomes easy for business players to maintain their position in…

Continue Reading Molecular Modeling Software for Chemistry Market Size, Scope And Forecast

Bioinformatics Salary Entry Level at Level

Bioinformatics Salary Entry Level. Similar to any other job, their salary will increase as they gain experience. What is the average salary of a bioinformatics scientist? Senior Software Engineer from www.dreamjobs.lk $31,220 to $37,970 per year. The estimated base pay is $109,228 per year….

Continue Reading Bioinformatics Salary Entry Level at Level

Digital Identity Solutions Market In-Depth Analysis including Development Strategy, Regional Analysis, Key Segmentation by Major Companies like IDEMIA, ForgeRock, Imageware Systems, Jumio, NEC, Samsung SDS

“ The global Digital Identity Solutions Market is an information rich representation of the current market developments that echo upward spike in growth numbers. Our team of research experts at Adroit Market Research has relied upon dedicated primary and secondary research methodologies to make accurate deductions of the market developments,…

Continue Reading Digital Identity Solutions Market In-Depth Analysis including Development Strategy, Regional Analysis, Key Segmentation by Major Companies like IDEMIA, ForgeRock, Imageware Systems, Jumio, NEC, Samsung SDS

Nucleic Acids Research Papers on DAVID Update, ChIP-Atlas, RNA Splicing Assay

Researchers at the Frederick National Laboratory for Cancer Research and the National Institutes of Health describe a 2021 update to the bioinformatics tool DAVID, designed for functional annotation and functional gene enrichment analyses. Along with updates to annotation types and other “Knowledgebase” features, the latest version of the DAVID Gene…

Continue Reading Nucleic Acids Research Papers on DAVID Update, ChIP-Atlas, RNA Splicing Assay

Qiime2 Exclude Seqs with FASTQ as query data.

Qiime2 Exclude Seqs with FASTQ as query data. 0 Hello, I am working with FASTQ files and I want to filter them based on the alignment with references sequences in FASTA format. I decided to use QIIME2 for this. So I imported both FASTA and FASTQ files to the required…

Continue Reading Qiime2 Exclude Seqs with FASTQ as query data.

How to install SageMath in Ubuntu Linux?

SageMath is a free and open-source software for mathematical computation. It is built on top of many existing open-source libraries which include NumPy, SciPy, Matplotlib, SymPy, Maxima, etc. SageMath provides a command-line interface, browser-based notebooks, and tools for embedding formulas in other documents. Its syntax is similar to Python. In…

Continue Reading How to install SageMath in Ubuntu Linux?

Medical Alert System/Personal Emergency Response System Market Size And Forecast

New Jersey, United States – Medical Alert System/Personal Emergency Response System Market Research Report provides you with detailed and accurate analysis to strengthen your position in the market. It provides the latest updates and powerful insights on the Medical Alert System/Personal Emergency Response System industry to help you improve your business…

Continue Reading Medical Alert System/Personal Emergency Response System Market Size And Forecast

Using QCTOOL v2 to process UK Biobank .bgen files

Using QCTOOL v2 to process UK Biobank .bgen files – why so slow? 0 I’m currently using QCTOOL v2 to process imputed .bgen files from UK Biobank, however they seem to be processing very slowly. Is this normal? My command is pretty basic; I’m filtering out a list of SNPs…

Continue Reading Using QCTOOL v2 to process UK Biobank .bgen files

Single cell database scrna dB for bioinformatics database development (1)

Single cell database construction High quality integrated single cell database If readers just want to get a ready-made single-cell database with rich content and add it to their own PC or linux The server , You can skip the following detailed theoretical tutorial Database download link : Click to download…

Continue Reading Single cell database scrna dB for bioinformatics database development (1)

Mapping back 3 sets of reads/sample with minimap2

I used FaQC to qc my raw fastqs before assembling. That program (and perhaps others) outputs properly paired Forward and Reverse fastqs, as well as an unpaired fastq file for each sample. I used the all 3 for each single sample assembly. Since minimap2 only allows for 2 query files,…

Continue Reading Mapping back 3 sets of reads/sample with minimap2

GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

Continue Reading GDCprepare of RNAseq counts produces error

How to edit a SAM file using pysam

How to edit a SAM file using pysam 0 Dear all – I have a template sam file and I want to change one of the columns (template_length) and replace it with a new value. The new value is a quick mathematical operation. template sam file: @HD VN:1.0 SO:unsorted @SQ…

Continue Reading How to edit a SAM file using pysam

What is ClustalW? Tutorial of How to Use ClustalW

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

Continue Reading What is ClustalW? Tutorial of How to Use ClustalW

RSQLite: binding sets and scalars in the same select query

Why do you specify y = I(list(7,6)) instead of y=c(6,7)? This seems to work: dbGetQuery (c, “select * from tst where x = ? and y in (?)”, data.frame(x=1, y=c(7,6))) You might be looking for expand.grid. dbGetQuery (c, “select * from tst where x = ? and y in (?)”,…

Continue Reading RSQLite: binding sets and scalars in the same select query

Introduction to the BLAST Suite and BLASTN | Michael Agostino

In Chapter 2 we learned how to search databases with text queries. All of these were exact matches—that is, we were expecting to find the exact accession number or exactly spelled words. In this chapter, a much harder database-searching problem is introduced. How do you find matches when your query…

Continue Reading Introduction to the BLAST Suite and BLASTN | Michael Agostino

BLASTn using R

BLASTn using R 0 Hello, I have around 2000 DNA nucleotide sequences (60 bases long) stored in each row in an excel sheet. I want to run BLAST over each one of them individually and extract the “Description” of the first hit. Like for Example: Suppose on NCBI BLAST website…

Continue Reading BLASTn using R

“No such file or directory: ‘test.xml”

Biopython NcbiblastpCommandline not working: “No such file or directory: ‘test.xml” 0 from Bio.Blast.Applications import NcbiblastpCommandline blastp=r”C:\NCBI\blast-BLAST_VERSION+\bin\blastp.exe” blastp_cline = NcbiblastpCommandline(blastp, query=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.fasta”, db=r’C:/NCBI/blast-BLAST_VERSION+/bin/bos_protein.fasta’, outfmt=5, evalue=0.00001, out=r”C:/NCBI/blast-BLAST_VERSION+/bin/test.XML”) blastp_cline from Bio.Blast import NCBIXML with open(“test.XML”) as result_handle: E_VALUE_THRESH=0.01 blast_records = NCBIXML.parse(result_handle) blast_record = NCBIXML.read(result_handle) for alignment in blast_record.alignments: for hsp in alignment.hsps: if hsp.expect…

Continue Reading “No such file or directory: ‘test.xml”

From scientific name to taxonomy information entrez

From scientific name to taxonomy information entrez 1 Hi all, I have a txt file with a list of scientific names of plants and I would like to obtain a final file with taxonomy information. For example, if one of my organism is Acalypha hispida, I would like to obtain…

Continue Reading From scientific name to taxonomy information entrez

AlphaFold, GPT-3 and How to Augment Intelligence with AI

This is the first post in a two-part series. Read Part 2 here. Around the same time that Alan Turing was shaping his theories of machine intelligence in Manchester, another future giant of the computing world, Douglas Engelbart, was developing an alternative computing paradigm over 5,000 miles away in…

Continue Reading AlphaFold, GPT-3 and How to Augment Intelligence with AI

Google Researchers Use Machine Learning Approach To Annotate Protein Domains

Source: www.nature.com/articles/s41587-021-01179-w.epdf Proteins play an important part in the construction and function of all living organisms. Each protein is made up of a chain of amino acid building blocks. Much like an image might have numerous things, a protein can have multiple components, known as protein domains. Researchers have been…

Continue Reading Google Researchers Use Machine Learning Approach To Annotate Protein Domains

Text string using Biopython – Stack Overflow

I’m using Biopython in my code and i need to extract the abstract out of articles. For searching the article I’m using the function: def search(query): Entrez.email=”your.email@example.com” handle = Entrez.esearch(db=’pubmed’, sort=”relevance”, retmax=’20’, retmode=”xml”, term=query) results = Entrez.read(handle) return results I’m looking for the simpliest way to get the text as…

Continue Reading Text string using Biopython – Stack Overflow

Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

Continue Reading Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics

We implemented a metagenomic DNA sequencing methodology to unbiasedly detect microbial species in CSF samples from patients with CNS symptoms in which a pathogen or EBV had been detected (Additional 3: Table 1). Samples positively identified with pathogen-specific quantitative PCR (qPCR), 16S rRNA gene sequencing or bacterial/mycotic culture in CSF…

Continue Reading Optimization of cerebrospinal fluid microbial DNA metagenomic sequencing diagnostics

biopython – How to blastp with fasta file that contains ~50 sequences

I’m trying to blastp multiple aminoacids sequences using biopython. I just can’t seem to get it right and i cant figure out the handbook for how to do this. I have come up with the following: open(“proteins_PROT.fasta”,”r”) from Bio.Blast.Applications import NcbiblastpCommandline cline = NcbiblastpCommandline(query=”proteins_PROT.fasta”, db=”nr”, evalue=0.001, remote=True, ungapped=True) NcbiblastpCommandline(cmd=’blastp’, query=”proteins_PROT.fasta”,…

Continue Reading biopython – How to blastp with fasta file that contains ~50 sequences

peroxisomal multifunctional enzyme type 2-like, maker-scaffold366_size194251-snap-gene-0.19 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of peroxisomal multifunctional enzyme type 2-like vs. L. salmonis genes Match: EMLSAG00000010112 (supercontig:LSalAtl2s:LSalAtl2s668:190059:194758:1 gene:EMLSAG00000010112 transcript:EMLSAT00000010112 description:”augustus_masked-LSalAtl2s668-processed-gene-1.1″) HSP 1 Score: 102.064 bits (253), Expect = 2.195e-25Identity = 65/191 (34.03%), Postives = 101/191 (52.88%), Query Frame = 0 Query: 134 GKVALVTGAGGGLGKAYALLLASRGASVVVNDLGGSRTGEGQSSKAADEVVNEIRQKGGKAV—–GNYDSVEDGEAVIKTALDNFGRIDIVINNAGILRDRSIGRTSDSDWDLVQKVHLRGAFQVIRAAWPHMKKQKYGRIINTSSVAGIFGNFGQSNYSSAKAGLIGLTSTLAIEGERSGIQANVIVP 319 GKVAL+TGA G+G++ A+L A…

Continue Reading peroxisomal multifunctional enzyme type 2-like, maker-scaffold366_size194251-snap-gene-0.19 (gene) Tigriopus kingsejongensis

use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

Continue Reading use tcgabiolinks package to download TCGA data

Substitute variables in an expression in Sagemath

Somewhat similar to this question, I was trying to evaluate a Boolean expression given the right hand side variables in Sage. For simplicity, say, my Boolean expression is, $y=x_0+x_1$. For each of $(x_0,x_1) in {(0,0),(0,1),(1,0),(1,1)}$, I want to evaluate $y$. This is the basic code block to get started. Note…

Continue Reading Substitute variables in an expression in Sagemath

How to Build a Code Search Tool Using PyTorch Transformers and Annoy | by Youness Mansar | Feb, 2022

Leveraging joint text and code embeddings for search. Modified from Photo by Markus Winkler on Unsplash Did you ever look for a code snippet on google because you were too lazy to write it yourself? Most of us did! Then how about building your own code search tool from scratch?…

Continue Reading How to Build a Code Search Tool Using PyTorch Transformers and Annoy | by Youness Mansar | Feb, 2022

Postdoctoral Fellowship in Bioinformatics/Statistics – UN Jobs Vacancies Tenders

*Applications may be reviewed on a rolling-basis and this posting could close before the deadline. ARS Office/Lab and Location: A postdoctoral fellowship in bioinformatics/statistics is currently available with the U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), Southern Regional Research Center located in New Orleans, Louisiana. Research Project: Food allergy costs the US $25…

Continue Reading Postdoctoral Fellowship in Bioinformatics/Statistics – UN Jobs Vacancies Tenders

A mammalian methylation array for profiling methylation levels at conserved sequences

Designing the mammalian methylation array The CMAPS algorithm is designed to select a set of Illumina Infinium array probes such that for a target set of species many probes are expected to work in each species (see “Methods” section). Array probes are sequences of length 50 bp flanking a target CpG…

Continue Reading A mammalian methylation array for profiling methylation levels at conserved sequences

AWS IoT Core Integration with NVIDIA DeepStream error in make command – #3 by AnamikaPaul – DeepStream SDK

Please provide complete information as applicable to your setup. • Hardware Platform (Jetson / GPU) Jetson nano• DeepStream Version 6.00• JetPack Version (valid for Jetson only)• TensorRT Version• NVIDIA GPU Driver Version (valid for GPU only)• Issue Type( questions, new requirements, bugs)• How to reproduce the issue ? (This is…

Continue Reading AWS IoT Core Integration with NVIDIA DeepStream error in make command – #3 by AnamikaPaul – DeepStream SDK

Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) – Global Variome shared LOVD

Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) Chromosome 17 Allele Unknown Affects function (as reported) Effect unknown Affects function (by curator) Not classified Classification method – Clinical classification VUS DNA change (genomic) (Relative to hg19 / GRCh37) g.7100169G>A DNA change (hg38) – Published as DLG4(NM_001321075.2):c.990C>T (p.G330=) ISCN – DB-ID DLG4_000038 Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION record Segregation – Frequency – Re-site –…

Continue Reading Variant #0000726648 (NC_000017.10:g.7100169G>A, ACADVL(NM_000018.3):c.-23135G>A) – Global Variome shared LOVD

Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) – Global Variome shared LOVD

Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) Chromosome 7 Allele Unknown Affects function (as reported) Effect unknown Affects function (by curator) Not classified Classification method – Clinical classification VUS DNA change (genomic) (Relative to hg19 / GRCh37) g.92730753A>G DNA change (hg38) – Published as SAMD9(NM_017654.3):c.4658T>C (p.I1553T), SAMD9(NM_017654.4):c.4658T>C (p.I1553T) ISCN – DB-ID SAMD9_000024 See all 3 reported entries Variant remarks VKGL data sharing initiative Nederland Reference – ClinVar ID – dbSNP ID – Origin CLASSIFICATION…

Continue Reading Variant #0000803285 (NC_000007.13:g.92730753A>G, SAMD9(NM_017654.3):c.4658T>C) – Global Variome shared LOVD

[slurm-users] Issues upgrading db from 20.11.7 -> 21.08.4

Hello! I’m trying to test an upgrade of our production slurm db on a test cluster. Specifically I’m trying to verify a update from 20.11.7 to 21.08.4. I have a dump of the production db, and imported as normal. Then firing up slurmdbd to perform the conversion. I’ve verified everything…

Continue Reading [slurm-users] Issues upgrading db from 20.11.7 -> 21.08.4

[gmx-users] why not coordinates from cpt file

Post by gromacs queryHi allI have very simple query. While continuing simulations why we need to use*.gro (-c) with grompp as *.cpt (-t) has all the information (as checkedwith gmxcheck)?cpt file should suffice all the purposes. I tried using grompp providing -t*.cpt file but without -c *.gro file, it does…

Continue Reading [gmx-users] why not coordinates from cpt file

[lammps-users] moving graphene as rigid – LAMMPS Mailing List Mirror

Hello LAMMPS users, I am using windows 30 july 2021. units are real. I have a query regarding rigid command. I want to move graphene as a rigid body. For this I have created two groups. One group is fixedatoms (purple colored) and the second group is rigidcarbonatoms (grey color)….

Continue Reading [lammps-users] moving graphene as rigid – LAMMPS Mailing List Mirror

How to convert transcript-relative coordinates to genomic coordinates?

How to convert transcript-relative coordinates to genomic coordinates? 0 I have queried using Entrez Utilities (efetch: www.ncbi.nlm.nih.gov/books/NBK25499/) and obtained annotations for transcripts like the following: >Feature ref|NM_152486.3| 1 2557 gene gene SAMD11 gene_syn MRS gene_desc sterile alpha motif domain containing 11 db_xref GeneID:148398 db_xref HGNC:HGNC:28706 db_xref MIM:616765 How/what database should…

Continue Reading How to convert transcript-relative coordinates to genomic coordinates?

taxonomy – Assign multiple taxids to a sequence when constructing a local BLAST database

I recently had a script fail due to poor handling of BLAST output. The BLAST -outfmt staxids field usually returns a single taxid, but occasionally it returns two or more taxids separated by a semicolon, such as 556514;701533. Fixing the script to handle this should be fairly straightforward. But the…

Continue Reading taxonomy – Assign multiple taxids to a sequence when constructing a local BLAST database

Install CUDA on NVIDIA Jetson Nano

Hardware Pre-requisite Jetson Nano A 5V 4Ampere Charger 64GB SD card Software Preparing Your Raspberry Pi Flashing Jetson SD Card Image Unzip the SD card image Insert SD card into your system. Bring up Etcher tool and select the target SD card to which you want to flash the image….

Continue Reading Install CUDA on NVIDIA Jetson Nano

Convert list of Accession Numbers to Full Taxonomy

Using NCBI Entrez direct. $ esearch -db assembly -query “GCA_000005845” | elink -target taxonomy | efetch -format native -mode xml | grep ScientificName | awk -F “>|<” ‘BEGIN{ORS=”, “;}{print $3;}’ Escherichia coli str. K-12 substr. MG1655, cellular organisms, Bacteria, Proteobacteria, Gammaproteobacteria, Enterobacterales, Enterobacteriaceae, Escherichia, Escherichia coli, Escherichia coli K-12, If…

Continue Reading Convert list of Accession Numbers to Full Taxonomy

downloading RNA seq data

downloading RNA seq data 0 Hi friends I am using the following code to get the data from TCGA. I want to have only one allocate of each person then I will have unique patients ID. Is there any line of code that I should add to this to get…

Continue Reading downloading RNA seq data

Bioconductor – GSE13015

DOI: 10.18129/B9.bioc.GSE13015     GEO accession data GSE13015_GPL6106 as a SummarizedExperiment Bioconductor version: Release (3.14) Microarray expression matrix platform GPL6106 and clinical data for 67 septicemic patients and made them available as GEO accession [GSE13015](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE13015). GSE13015 data have been parsed into a SummarizedExperiment object available in ExperimentHub. This data data…

Continue Reading Bioconductor – GSE13015

[lh3/minimap2] Memory leak when using Python and threads

The program align.py uses mappy to align reads in Python using multiple worker threads. After loading the index the memory usage jumps up quickly to >20Gb and then continues to climb steadily through 40Gb an beyond. This issue was first discovered in bonito and isolated to mappy. The data flow…

Continue Reading [lh3/minimap2] Memory leak when using Python and threads

Bwa on multiple processor

Hi Guys, When I am trying to run bwa mem on multiple processor, I am getting error as : > mpirun -np 16 bwa mem hg19-agilent.fasta R1.fastq R2.fastq | samtools sort -o aln.bam [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read 0 ALT contigs [M::bwa_idx_load_from_disk] read…

Continue Reading Bwa on multiple processor

Introducing CreateAPI | kean.blog

If you’ve tried OpenAPI spec generators, you know how it goes. They get you about 60-80% there, but you end up having to modify the code by hand. For one of the specs (GitHub REST API spec), a popular code generator I tried produced more than 300 compile-time errors. With…

Continue Reading Introducing CreateAPI | kean.blog

VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

Describe the issue VEP give errors even my query and reference has same assembly version Command :$: ./vep -i examples/homo_sapiens_GRCh37.vcf –cache –refseq cache reference details while running install.pl ? 458 NB: Remember to use –refseq when running the VEP with this cache! downloading ftp.ensembl.org/pub/release-104/variation/indexed_vep_cache/homo_sapiens_refseq_vep_104_GRCh37.tar.gz unpacking homo_sapiens_refseq_vep_104_GRCh37.tar.gz converting cache, this may…

Continue Reading VEP issue: ERROR: Cache assembly version (GRCh37) and database or selected assembly version (GRCh38) do not match

BLAST | ICGRC

In bioinformatics, BLAST (Basic Local Alignment Search Tool) is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. A BLAST search enables a researcher to compare a query sequence with a library or database of sequences, and…

Continue Reading BLAST | ICGRC

makeblastdb creating multiple files of unexpectedly large sizes

I have a set of 100 amino acid sequences and I want to perform a BLASTP sesrch against the refseq_protein database. Accordingly I had set up the standalone version of BLAST (Version 2.11.0+) and downloaded the refseq_protein database from NCBI using the following code wget ftp.ncbi.nlm.nih.gov/refseq/release/complete/*.faa.gz The database gets downloaded…

Continue Reading makeblastdb creating multiple files of unexpectedly large sizes

sra toolkit

sra toolkit 1 hello I cannot download sra files. I tried prefetch SRR17055838 and gives this error 2021-12-26T13:48:20 prefetch.2.11.2 err: error unexpected while resolving query within virtual file system module – failed to resolve accession ‘SRR17055838’ – The object is not available from your location. ( 406 ) 2021-12-26T13:48:20 prefetch.2.11.2:…

Continue Reading sra toolkit

The Hot Topic In Probabilistic Programming

One of the biggest challenges of this decade is solving uncertainty, ethical and explainable problems in the thousands of machine learning models we interact with daily. Meta, formerly Facebook, announced the release of their supplement to aid this developing sphere. Bean Machine, Meta’s probabilistic programming system, is a PyTorch-based model…

Continue Reading The Hot Topic In Probabilistic Programming

How do I “flush” data to my RSQLite disk database?

You’re not using the pattern suggested by the RSQLite documentation. That documentation uses dbWriteTable to copy a data frame into a SQLite table: dbWriteTable(con, “mtcars”, mtcars) According to this documentation, your full code would look something like this: con <- dbConnect(RSQLite::SQLite(), “./mtcars.db”) data(mtcars) dbWriteTable(con, “mtcars”, mtcars) dbListTables(con) # Fetch all…

Continue Reading How do I “flush” data to my RSQLite disk database?

GSA – Galaxy Community Hub

Galaxy-GSA – Galaxy Community Hub ← Platform Directory comments Gene Set Analysis (GSA) can be defined as the comparison of a query gene set (a list or a rank of differentially expressed genes, for example) to a reference database of annotated gene sets, in order to interpret the initial query…

Continue Reading GSA – Galaxy Community Hub

Delightful code generation for OpenAPI specs for Swift written in Swift

Delightful code generation for OpenAPI specs for Swift written in Swift. Fast: processes specs with 100K lines of YAML in less than a second Smart: generates Swift code that looks like it’s written by hand Reliable: tested on 500K lines of publically available OpenAPI specs producing correct code every time…

Continue Reading Delightful code generation for OpenAPI specs for Swift written in Swift

Automation Hub Open API Power Query Data Parsing

Parsing the data from the Automation Hub API can sometimes prove to be challenging, especially if you are consolidating a very complex report. In this page, we are presenting a couple of tips and tricks that can be used to improve the overall data parsing process. The page contains: The…

Continue Reading Automation Hub Open API Power Query Data Parsing

RStudio AI Weblog: Picture segmentation with U-Internet

Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…

Continue Reading RStudio AI Weblog: Picture segmentation with U-Internet

bioinformatics – Local BLAST NCBI C++ Exception

I’m getting an error trying to to use blast v2.12 against a local nt database. I’ve downloaded nt twice from the ftp server thinking the first time it was corrupt but that didn’t change anything. My command is: blastn -db nt -num_threads 8 -outfmt “6 qseqid sacc stitle ssciname nident…

Continue Reading bioinformatics – Local BLAST NCBI C++ Exception

40231867-SWI-Prolog-as-a-Semantic-Web-Tool-for-semantic-querying-in-Bioclipse-Integration-and-perfor – SWI-Prolog as a Semantic Web Tool for semantic

Unformatted text preview: SWI-Prolog as a Semantic Web Tool for semantic querying in Bioclipse: Integration and performance benchmarking Samuel Lampa June 2, 2010 Abstract The huge amounts of data produced in new high-throughput techniques in the life sciences, and the need for integration of heterogeneous data from disparate sources in…

Continue Reading 40231867-SWI-Prolog-as-a-Semantic-Web-Tool-for-semantic-querying-in-Bioclipse-Integration-and-perfor – SWI-Prolog as a Semantic Web Tool for semantic

Postdoctoral Position in Structural Bioinformatics job with National Institute of Allergy and Infectious Diseases (NIAID)

  Postdoctoral Position in Structural Bioinformatics Department of Health and Human Services National Institutes of Health National Institute of Allergy and Infectious Diseases The Structural Bioinformatics Core Section (SBIS) at the National Institute of Allergy and Infectious Diseases (NIAID), Vaccine Research Center (VRC), located on the main National Institutes of…

Continue Reading Postdoctoral Position in Structural Bioinformatics job with National Institute of Allergy and Infectious Diseases (NIAID)

python – Directly referring to database tables in DataSpell (?)

I downloaded DataSpell, configured Jupyter Notebook (works) and connected to the database which I’m using (works). Is there any way now how I can directly refer to chosen tables in the database (via DataSpell environment) or do I still need to write whole connection code inside Jupyter Notebook? E. g….

Continue Reading python – Directly referring to database tables in DataSpell (?)

Single-cell delineation of lineage and genetic identity in the mouse brain

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

Continue Reading Single-cell delineation of lineage and genetic identity in the mouse brain

How to differenciate between 16s hypervariables regions using QIIME2 ? – User Support

M_F: May i search the sequences on ncbi for example correponding to v4 domain No, NCBI probably would not have such sequences in an easily indexed form but I could be wrong. Rather, grab some reference sequences (can be a random subsample, do not need all of them) and use…

Continue Reading How to differenciate between 16s hypervariables regions using QIIME2 ? – User Support

KINNEY_DNMT1_METHYLATION_TARGETS

Standard name KINNEY_DNMT1_METHYLATION_TARGETS Systematic name M2508 Brief description Hypomethylated genes in prostate tissue from mice carrying hypomorphic alleles of DNMT1 [GeneID=1786]. Full description or abstract Previous studies have shown that tumor progression in the transgenic adenocarcinoma of mouse prostate (TRAMP) model is characterized by global DNA hypomethylation initiated during early-stage…

Continue Reading KINNEY_DNMT1_METHYLATION_TARGETS

laboratory jobs in germany

We wish you a good luck and have a prosperous career. Working at Labcorp | Jobs and Careers at Labcorp 15 GNeuS Postdoc Positions in Neutron Science of 24 Months Each (Full-time Job) FZJ – Forschungszentrum Jülich. What other similar jobs are there to Laboratory jobs in Germany? Clinical Laboratory…

Continue Reading laboratory jobs in germany

A pandemic-scale phylogenetic analysis tool

Phylogenetics is an analytical tool that quickly analyzes genomic data to provide invaluable insights into the evolution and spread of a pathogen, thereby allowing public health officials and governments to respond to it in a timely fashion. During the coronavirus disease 2019 (COVID-19) pandemic, phylogenetics, like many other pre-pandemic tools,…

Continue Reading A pandemic-scale phylogenetic analysis tool

Blast command line pipeline not working

Blast command line pipeline not working 0 Hello, I am running now a local blast pipeline using MacOs. The goal here is to take interval of the 5 best hits and then extract the SNP variants from multiple vcf.gz files. But I am facing an error which I cannot solve….

Continue Reading Blast command line pipeline not working

Easy OpenAPI specs and Swagger UI for your Flask API

Easy Swagger UI for your Flask API Flasgger is a Flask extension to extract OpenAPI-Specification from all Flask views registered in your API. Flasgger also comes with SwaggerUI embedded so you can access localhost:5000/apidocs and visualize and interact with your API resources. Flasgger also provides validation of the incoming data,…

Continue Reading Easy OpenAPI specs and Swagger UI for your Flask API

Piranha Peak-Calling with multiple replicates

Piranha Peak-Calling with multiple replicates 0 I am trying to call RNA-Protein interation peaks by using Piranha software. I have multiple replicates for each experiment and the control data, and I can’t seem to understand how to combine them into one Piranha query. For example, if I was to call…

Continue Reading Piranha Peak-Calling with multiple replicates

Dedupe array of database results

A result set from a PDO query is as follows… Array ( [0] => Array ( [activity_link_type] => Category [data_id] => 1 ) [1] => Array ( [activity_link_type] => Category [data_id] => 38 ) [2] => Array ( [activity_link_type] => PData [data_id] => 108 ) [3] => Array ( [activity_link_type]…

Continue Reading Dedupe array of database results

alphafold2: HHblits failed – githubmemory

I’ve tried using the standard alphafold2 setup via docker (converted to a singularity container) via the setup described at github.com/kalininalab/alphafold_non_docker, and both result in the following error: […] E1210 12:01:01.009660 22603932526400 hhblits.py:141] – 11:49:18.512 INFO: Iteration 1 E1210 12:01:01.009703 22603932526400 hhblits.py:141] – 11:49:19.070 INFO: Prefiltering database E1210 12:01:01.009746 22603932526400 hhblits.py:141]…

Continue Reading alphafold2: HHblits failed – githubmemory

What is the single nucleotide polymorphism database ( dbsnp )?

The Single Nucleotide Polymorphism Database (dbSNP) is a free public archive for genetic variation within and across different species developed and hosted by the National Center for Biotechnology Information (NCBI) in collaboration with the National Human Genome Research Institute (NHGRI). Furthermore, are there any databases for single nucleotide polymorphisms?As there…

Continue Reading What is the single nucleotide polymorphism database ( dbsnp )?

Malaysian Genomics dives to lowest in nine months after hitting limit down

KUALA LUMPUR (Dec 9): Malaysian Genomics Resource Centre Bhd’s (MGRC) share price hit limit down on Thursday (Dec 9, 2021) after the health technology company’s stock price fell as much as 35 sen or 29.91% to 82 sen. At 82 sen, MGRC’s share price is at its lowest in about…

Continue Reading Malaysian Genomics dives to lowest in nine months after hitting limit down

r – Is there a way to do a negative match using regex sub?

Say I have a vector of strings, g<-c(“bunchofstuff>query=true/fun/weird>bunchofstuff”, “bunchofstuff>query=animals/octopus/weird>bunchofstuff”, “bunchofstuff>query=flowers/sunshine/fun>bunchofstuff”, ” bunchofstuff>query=fun/true/sunshine>bunchofstuff” and I want to essentially use sub to erase anything after query=, until the end of the string, IF query= is not followed by true (ideally in any position). As far as I can tell, there isn’t a…

Continue Reading r – Is there a way to do a negative match using regex sub?

Help needed for Ensembl Gene ID conversion for RNA-seq data

Hello All, I am new to the RNA-seq world and especially new to the bioinformatics side. We recently completed a RNA-seq experiment (total RNAs) on human samples and we used illumina’s Dragen RNA pipeline which generated salmon gene count (.sf) output files. In the files, the gene ID is in…

Continue Reading Help needed for Ensembl Gene ID conversion for RNA-seq data

Bash script to help with print Name of reads that only have query subsequence or its verse complement and position of first occurance of this subsequence in read and output of all this in tab separat

Bash script to help with print Name of reads that only have query subsequence or its verse complement and position of first occurance of this subsequence in read and output of all this in tab separat 0 Create bash script that receives name of fastq fastq file and query subsequence…

Continue Reading Bash script to help with print Name of reads that only have query subsequence or its verse complement and position of first occurance of this subsequence in read and output of all this in tab separat

Curio Genomics Joins the International Wheat Genome Sequencing Consortium

Newswise — The International Wheat Genome Sequencing Consortium (IWGSC) is pleased to announce that the bioinformatics company Curio Genomics has joined the organization as a sponsoring partner. The IWGSC is an international, collaborative consortium of wheat growers, plant scientists, and public and private breeders dedicated to the development of genomic…

Continue Reading Curio Genomics Joins the International Wheat Genome Sequencing Consortium

r – RSQlite – Find values with most occurences in group

I’m using RSQlite to import Datasets from an SQlite-Database. There are multiple millions of observations within the Database. Therefor I’d like to do as much as possible of Data selection and aggregation within the Database. At some point I need to aggregate a character variable. I want to get the…

Continue Reading r – RSQlite – Find values with most occurences in group

How to call variant by –max-depth for RNAseq

Hi everyone! I have a query regarding variant calling from a high coverage site on the basis of the maximum likelihood variant. I have RNA-seq data mapped bam file. I called variant using the below command. “bcftools mpileup –max-depth 10000 -Oz -f ref.fa sample.bam | bcftools call -mv -Oz -o…

Continue Reading How to call variant by –max-depth for RNAseq