Tag: BED

Hi Everyone, I have a genotype file in  .pgen  format, that I subset and would like to calculate LD Matrix for. Previously I used a .bed file format and use plink 1.9 which worked as charm. But unfortunately my file is in Pgen format which is not supported  in plink…

A novel STR panel for human protein-coding genes To explore STR mutations in CRC, we first annotated STRs in the introns, exons, and promoter sequence of all protein-coding genes in the GRCh38 reference genome (“Methods”). We discarded STR loci for which genotyping was expected to be inaccurate due to genomic…

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

Problem with DRAGEN RNAseq hashtable directory 1 Dear all, Recently I wrote a code to work with DRAGEN and RNAseq pipeline. I use this command: /opt/edico/bin/dragen -f -l \ -r refdir \ -1 ${forward} \ -2 ${reverse} \ -a ${gtf} \ –output-dir output/${sample} \ –output-file-prefix ${sample} \ –RGID ${sample}_group_id \…

It’s the holiday season, and what’s better to do than cuddle up in bed and watch a movie? We want to make sure you’re not missing out on some binge-worthy biotech movies this December. So, we have created a watchlist just for you. Here are some biotech movie recommendations to…

My paired end data became single end data after mapping 1 Dear community, Something weird happened to me, my public dataset is obviously paired-end data (stated in ‘metadata’ part of ENA database, and there are two seperate fastq files (R1 & R2) and index file (I1) per sequencing run). After…

Search for specific SNPs in VCF files of patients. 0 I have 490 genomes from 490 patients in VCF format. I created a Multi VCF file from these VCFs. I want to find 2 mutations (Y215C and G325R) in these patients, count the number of patients who have these SNPs…

Alston JM, Sambucci O. Grapes in the world economy. In: Cantu D, Walker MA, editors. The grape genome. Springer International Publishing; 2019. p. 1–24. Google Scholar  Rahemi A, Dodson Peterson JC, Lund KT. Grape rootstocks and related species. Cham: Springer International Publishing; 2022. Walker MA, Heinitz C, Riaz S, Uretsky…

Study objectives and endpoints The main objective consisted in identifying predictive biomarkers of efficacy by exploring correlation between baseline potential biomarkers and radiological and metabolic responses to afatinib. Secondary objectives were to identify potential pharmacodynamic biomarkers, to evaluate the efficacy and safety of afatinib and to assess the metabolic and…

Otto, S. P. & Whitton, J. Polyploid incidence and evolution. Annu. Rev. Genet. 34, 401–437 (2000). Article  CAS  PubMed  Google Scholar  Van de Peer, Y., Maere, S. & Meyer, A. The evolutionary significance of ancient genome duplications. Nat. Rev. Genet. 10, 725–732 (2009). Article  PubMed  Google Scholar  Comai, L. The…

Enrichment profiles from counts 0 Hello everyone, I’m currently working with single-cell DamID datasets, focusing on studying protein-DNA interactions. In my dataset for each cell, I have aligned BAM files, counts files in HDF5 format, and count files binned at 100kb intervals. These count files contain the number of unique…

Master forecasting models with Vertex AI Introduction Applications of FoRecasting Types of Data Sets for Forecasting UnivAriate Data Sets Multivariate Data Sets Forecasting Algorithms Statistical Methods ARIMA Models ARIMA plus Model with BQML Machine Learning Models Tree-Based Methods Neural Networks AdVantages of Neural Networks in Forecasting HANDling Cold Starts Cross-Learning…

Convert bed file from hg19 to GRCH38 1 Hello everyone! I have a list of over 500,000 rs and I would like to obtain the coordinates (BED file) on the GRCH38 reference genome. I am using the UCSC Table Browser tool, but unfortunately, it doesn’t find 90,000 rs, and since…

UPMC Presbyterian is hiring a full-time Bioinformatics Scientist to support the Molecular & Genomic Pathology Lab! This role will be scheduled for daylight shifts, Monday-Friday. The Molecular & Genomic Pathology Laboratory is a dynamic, state-of-the-art clinical laboratory that prides itself on delivering the highest quality of patient care through cutting-edge…

Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…

how to use multiple command in one line with using the output of last command to the next 0 I want to use several command in linux, and for second command i want to use the output of first and etc. I have tried this but im not sure that…

Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…

Your question is not completely clear, but since the most sensible ways to understand it have the same answer, I’m gonna go with that. I have the exact reference fasta used for generating the VCFs TLDR: You don’t have enough information to do this with just VCFs and reference fasta….

Mouse brain tissues All experimental procedures using live animals were approved by the Salk Institute Animal Care and Use Committee under protocol number 18-00006. Adult (P56) C57BL/6J male mice were purchased from the Jackson Laboratory at 7 weeks of age and maintained in the Salk animal barrier facility on 12-h dark–light…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Putnam, N. H. et al. Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317, 86–94 (2007). Article  ADS  CAS  PubMed  Google Scholar  Chapman, J. A. et al. The dynamic genome of Hydra. Nature 464, 592–596 (2010). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Srivastava, M….

Extract fasta sequence from gff3 file 2 Hi everyone, I have a lot of .gff3 files with the CDS features and below with the fasta sequence. This sequence is separated from the CDS features like this: ##FASTA >NZ_NZ_LR130533.1 I would like to extract all the fasta sequence into new fasta…

Hi Chris, I have a vcf file for which I have left aligned and split multi-allelic sites. Then used, plink2 –vcf test.vcf –make-bed –out test1; this gives me binaries file. then, I updated FID and sex (all males, all founders). In plink2 plink2 –bfile test1 –max-maf 0.01 –geno 0.05 –make-bed…

World Health Organization (WHO). WHO malaria report. 2022 www.who.int/publications/i/item/9789240064898 (2022). Savi, M. K. An overview of malaria transmission mechanisms, control, and modeling. Med. Sci. 11, 3 (2023). Google Scholar  Bahk, Y. Y. et al. Epidemiological characteristics of re-emerging vivax malaria in the Republic of Korea (1993–2017). Korean J. Parasitol. 56,…

extract variants from 1000 Genome VCF files 0 Hi everyone, I have a gVCF containing genetic information from different individuals, and I would like to extract specific SNPs. The SNPs of interest are listed in a BED file with the following structure (the end position rapresent the real position of…

by Ramya Ravi, Susan Kahler at Intel Lightning Talk 1: Seismic Data to Subsurface Models with OpenFWI Speaker: Benjamin Consolvo, AI Software Engineering Manager, Intel, LinkedIn Session Overview In this session, Ben begins with an overview of seismic imaging and full waveform inversion (FWI). Seismic imaging and FWI helps us…

Zachos, J., Pagani, H., Sloan, L., Thomas, E. & Billups, K. Trends, rhythms, and aberrations in global climate 65 Ma to present. Science 292, 686–693 (2001). Article  ADS  CAS  PubMed  Google Scholar  Favre, A. et al. The role of the uplift of the Qinghai-Tibetan Plateau for the evolution of Tibetan…

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Istvan Albert, cmdcolin, and was edited by…

“Unlock Your Potential: Join AstraZeneca as a Bioinformatics Consultant and Revolutionize Drug Discovery!” –Must See– AstraZeneca Bioinformatics Job Job Post: Consultant – Bio Informatician At AstraZeneca, our mission is to improve the quality of healthcare and make a positive impact on the lives of millions of patients. We are seeking…

GetPileupSummaries intervals-list with Targeted Sequencing? 0 Hi! I am applying the GetPileUpSummaries, for somatic variant calling starting from targeted sequencing .fasta. I aligned the file with the GrCh38 reference. And currently I am at the GetPileUpSummariesStep. gatk –java-options -Xmx200G GetPileupSummaries \ -I $RECBAM \ -L ???? \ -O $OUTPUT \…

Infer ancestry for RNA-seq data 0 I generated VCF files with bcftools for 4 patient RNA-seq samples. I was also able to generate bed, bim, and fam files with PLINK for these files. I want some guidance on how to infer ancestry for these RNA-seq samples: How do I find…

Converting txt.gz to PLINK bim 0 Hello, I’m trying to do a stratified LDSC (or S-LDSC/partitioned LDSC) between locus of interest and diseases (diabetes, arthritis, etc.). For locus of interest, I have a bed file from previous research. For diseases, I have downloaded GWAS sumstats from the GWAS atlas. I…

DescriptionLinseis L6514 Flat Bed Graph Lab Chart RecorderRecorder has been tested working and is guaranteed fully functional.Item has heavy wear from previous use including scuffs, scratches and blemishes.Power cord not included.Photos of actual item for sale.Item is on hand and ready to ship.Please feel free to message us if you…

The PrEPVacc trial has stopped administering two investigational HIV vaccines that showed no efficacy in preventing infection, investigators announced on Wednesday during the International Conference on AIDS and STIs in Africa in Zimbabwe. “Vaccinations to PrEPVacc trial participants have been stopped because an analysis of the data collected so far…

The first PrEPVacc volunteer participant receives an injection at the launch of the launch of the PrePVacc Trial at the Masaka site of the MRC/UVRI and LSHTM Uganda Research Unit, on Tuesday 15 December 2020. Credit: PrEPVacc Investigators The PrEPVacc HIV prevention study of experimental vaccine regimens and a new…

In this article, Analytik Jena details what technology can make protein purification less variable and faster with the help of liquid-handling equipment. The CyBio FeliX and PhyTips® can conduct 96 targeted protein purifications in 120 minutes, requiring no hands-on time. These products are intended for drug discovery professionals in the…

Hi! I have been RNA seq short read sequencing data for a 112 dengue samples. I need to know by what percentage transcriptome is covered by our sequencing reads? I found Bedtools as an appropriate tool for this. however, i am unable to understand two different outputs from this tool…..

This gadget looks like a precursor to the devices medical officers use to scan patients in science fiction, and it is not far off. The MyotonPRO tests muscle tension and stiffness. The device is being used on the International Space Station by ESA astronaut Alexander Gerst. Part of the Myotones…

Given files genes.bed and snps.bed, you could do something like: $ bedmap –echo –echo-map-id –delim ‘\t’ genes.bed snps.bed > answer.bed The file answer.bed will contain the gene annotation and a semi-colon delimited list of SNP identifiers that overlap each gene. In order to get genes.bed, you could use Gencode v44…

PrEPVacc, the only current large HIV vaccine study, has been halted ahead of schedule because “there is little or no chance of the trial demonstrating vaccine efficacy in preventing HIV acquisition,” according to a December 6 announcement. Trial leaders shared the news at the International Conference on AIDS and STIs…

Company DescriptionGenomics England partners with the NHS to provide whole genome sequencing diagnostics. We also equip researchers to find the causes of disease and develop new treatments – with patients and participants at the heart of it all. Our mission is to continue refining, scaling, and evolving our ability to…

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Market Overview and Report Coverage \n…

Giga Shanghai To Expand, Phase 3, For Compact Car According to local media sources in China, Tesla is reported to be expanding its Giga Shanghai factory as it expands and prepares to produce the compact car, or $25,000 vehicle, or Model 2 – however you want to call it. The…

In this tutorial we learn how to install bedtools on Debian 11. bedtools is suite of utilities for comparing genomic features Introduction In this tutorial we learn how to install bedtools on Debian 11. What is bedtools bedtools is: The BEDTools utilities allow one to address common genomics tasks such…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Mon, 04 Dec 2023 20:13:11 +0100 Source: bedtools Architecture: source Version: 2.31.1+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1043957 Changes: bedtools (2.31.1+dfsg-2) unstable; urgency=medium . * d/clean: new: remove test/getfasta/t.fa.gz.gzi. (Closes: #1043957)…

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Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

Company Description Genomics England partners with the NHS to provide whole genome sequencing diagnostics. We also equip researchers to find the causes of disease and develop new treatments – with patients and participants at the heart of it all. Our mission is to continue refining, scaling, and evolving our…

Summary The all-new 2024 Toyota Tacoma SR trim level offers modern technology and functionality, including color-matched bumpers and LED headlights. The interior of the Tacoma SR is equipped with Toyota’s latest software, offering wireless Android Auto and Apple CarPlay, as well as Toyota Safety Sense 3.0 for enhanced safety. The…

Key Takeaways The 2024 Toyota Tacoma will start at $31,500, making it one of the most affordable pickup trucks in its segment. The base SR trim comes with a turbocharged 2.4-liter four-cylinder engine, producing 228 hp and 243 lb-ft of torque. The TRD Pro and Trailhunter versions of the Tacoma…

This is probably a duplicated question from: How To Convert Bed Format To Gtf? How to convert original BED file to a GTF ? Converting different annotation file formats (GTF/GFF/BED) to each other How to change scaffold.fasta file or scaffold.bed file to GTF file? Convert bed12 to GFF convert bed12…

Compute matrix skipping many regions stating not found in compute matrix output 0 Hello all I am working on Chip seq data and for generating the TSS Plots when I am computing the matrix it is giving a very long list stating “skipping NR_049895_r4, due to being absent in the…

No, it’s not included in the price. Range Anxiety The Cybertruck is finally here — and it’s a far cry from what was originally promised by CEO Elon Musk just over four years ago. The stainless steel pickup’s disappointing range, in particular, highlights the many compromises Tesla had to make…

No, your eyes are not deceiving you. The Tesla Cybertruck is finally here. The production-spec electric pickup was revealed at an event at Tesla’s Gigafactory in Austin, Texas, that was livestreamed on X, formerly known as Twitter. CEO Elon Musk started off the event by proclaiming, “You have a car…

Breadcrumb Trail Links Preview Pickup trucks New Vehicles Electric Vehicles Turns out a “Cyberbeast” trim will apparently offer more than 700 km on a charge thanks to a range extender Published Nov 30, 2023  •  Last updated 1 day ago  •  4 minute read The Tesla Cybertruck on display at the…

Tesla has finally revealed the pricing, range, trims, and other specifications of the Cybertruck at its delivery event at Gigafactory Texas today, as it handed over the first units to customers on Thursday afternoon. After four years, Tesla finally made the first deliveries of the Cybertruck in what will be…

Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article  ADS  CAS  Google Scholar  Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…

Introduction Oxford Nanopore Technologies (ONT) direct RNA sequencing (Fig 1A) enables detection of RNA modifications. A modified base produces an altered electrical current and/or dwell time relative to a canonical base that can be detected with algorithms (Garalde et al, 2018; Smith et al, 2019; Workman et al, 2019). Figure…

Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…

I need to soft-clip the primers of my amplicon reads and I have the following problem In scenario 1 I have forward and reverse reads in the same coordinates and I only want to soft-clip the first bases of each read (as shown in the example below) becaouse the reads…

CHIPSEQ Analysis , DiffBind Parameters 0 Hello, Regarding Diffbind, How does diffbind calculate common peaks with the samples. I’m observing that certain peaks identified as common using bedtools intersect are not appearing in the output report file generated after DiffBind analysis Command used to write the file : res_deseq <-…

Analysis of Roche KAPA Target Enrichment kit experimental data obtained on an Illumina sequencing system is most frequently performed using a variety of publicly available, open-source analysis tools. The typical variant calling analysis workflow consists of sequencing read quality assessment, read filtering, mapping against the reference genome, duplicate removal, coverage…

I’m trying to get a PRS for a very small subset of samples (~400 training, ~200 testing). Firstly I C+T the training data previous to PRSice. My .log is PRSice 2.3.3 (2020-08-05) github.com/choishingwan/PRSice(C) 2016-2020 Shing Wan (Sam) Choi and Paul F. O’ReillyGNU General Public License v3If you use PRSice in…

Abstract While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2–27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal…

(UroToday.com) The 2023 Society of Urologic Oncology (SUO) annual meeting held in Washington, D.C. between November 28th and December 1st, 2023, was host to a prostate cancer course. Dr. Alan Bryce provided an overview of the use and application of serial next generation sequencing (NGS) in the castrate-resistant prostate cancer disease…

Barnett R. Schistosomiasis. (1474–547X (Electronic)). Steinmann P, Keiser J, Bos R, Tanner M, Utzinger J. Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk. Lancet Infect Dis. 2006;6(7):411–25. Article  PubMed  Google Scholar  Uthailak N, Adisakwattana P, Thiangtrongjit T, Limpanont Y, Chusongsang P, Chusongsang Y, et…

The term “DNA,” once used only by scientists, has become part of our everyday lexicon. It’s almost impossible to not know of DNA profiling, from the court system to genealogy. It’s also nearly impossible to be unaware of the controversy. Now that we can each have a profile that identifies…

Van Valen, L. A new evolutionary law. Evol. Theory 1, 1–30 (1973). Google Scholar  Woolhouse, M. E. J., Webster, J. P., Domingo, E., Charlesworth, B. & Levin, B. R. Biological and biomedical implications of the co-evolution of pathogens and their hosts. Nat. Genet. 32, 569–577 (2002). Article  CAS  PubMed  Google…

Irish, S. R., Kyalo, D., Snow, R. W. & Coetzee, M. Updated list of Anopheles species (Diptera: Culicidae) by country in the Afrotropical Region and associated islands. Zootaxa 4747(3), 401–449. doi.org/10.1646/zootaxa.4747.3.1 (2020). Article  Google Scholar  Jacques, B. Les moustiques de l’archipel Comores. Série Entomologie Médicale et Parasitologie 15(2), 153–170 (1977)….

Bedtools intersection 0 While intersecting a VCF file and bed to obtain the reads that map to a class of genes, bedtools gives the following error: ***** WARNING: File TARGT_First.bed has inconsistent naming convention for record: chr1 45794952 45795134 MUTYH 1 ***** WARNING: File TARGT_First.bed has inconsistent naming convention for…

I am working on Chip seq data, I have implemented the chipseq pipeline with spike in method and called peaks using MACS2. The same data has been analyzed before in my lab, and my peaks show a similar pattern as the previous ones . By this I meant that the…

Analyzing genomic data, from sequences to structures, is a critical aspect of bioinformatics. Python has a rich ecosystem of tools and libraries specifically designed for genomic data analysis. Here’s an overview of key tools and libraries for various stages of genomic data analysis: Description: Biopython is a comprehensive open-source collection…

Institue for Health Metrics and Evaluation. Global Burden of Disease. vizhub.healthdata.org/gbd-results/ 2019. Troeger, C. E. et al. Quantifying risks and interventions that have affected the burden of diarrhoea among children younger than 5 years: an analysis of the Global Burden of Disease Study 2017. Lancet Infect. Dis. 20, 37–59 (2020)….

We’ve reached the final face-off of the race, as both Liquid and Echo are on Fyrakk and progressing side-by-side! They day didn’t see that much movement percentage-wise, but a whole lot of it fight mechanics-wise. Echo managed to catch up during the day and when Liquid came back the two…

I’m new to PLINK and I would like to obtain a file with SNPs in approximate linkage equilibrium. Here is my script and the outputs of each step. If someone could tell me if there is an error in the script because at…

Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…

BWA mem align reads with MQ = 0 to only one region (reference genome has two similar sequences). 1 So, i use WBA mem to align my reads (from NGS panels) to reference genome. My reads align to two different, but very similar regions. I want to prevent align these…

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

I was successful in running the first three commands of HINT ATAC as shown below following this tutorial github.com/sufyazi/sufyazi.github.io/wiki/TF-Footprinting-Tutorial-using-HINT-ATAC-module-from-RGT-toolbox rgt-hint footprinting –atac-seq –paired-end –organism=mm10 –output-location=/XXX –output-prefix=Afootprints A.mRp.clN.sorted.bam A.mRp.clN_peaks.narrowPeak rgt-hint footprinting –atac-seq –paired-end –organism=mm10 –output-location=/XXX –output-prefix=Afootprints B.mRp.clN.sorted.bam B.mRp.clN_peaks.narrowPeak rgt-motifanalysis matching –organism=mm10 –input-files Afootprints.bed Bfootprints.bed But when I ran the command below…

Hi all, I am a newbie in ChIP-seq, and I conducted my analysis using the nfcore ChIPseq pipeline. After reviewing the results, I now need to perform more specific analyses. With nfcore, I generated informative heatmaps that provide a general overview of my ChIP-seq data (I will upload the heatmap)….

How to overlap patient VCF with ClinVar database annotation using bedtools? 1 Hello, I’m trying to help a colleague who is trying to add ClinVar databases clinical significance column to VCF samples that she analysed. More specifically, we are trying to add overlapping/common variant annotation so that if the variant…

Circos karyotype file 1 Hi, I’m trying to generate some circos plots for structural variants, using the tool circos. To this I understand I need to specify a karyotype file. Please correct me if I’m wrong. But my understanding is that I need to create this karyotype file for GRCh38?…

Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Sat, 18 Nov 2023 16:34:59 +0100 Source: bedtools Architecture: source Version: 2.31.0+dfsg-2 Distribution: unstable Urgency: medium Maintainer: Debian Med Packaging Team <debian-med-packag…@lists.alioth.debian.org> Changed-By: Étienne Mollier <emoll…@debian.org> Closes: 1055414 Changes: bedtools (2.31.0+dfsg-2) unstable; urgency=medium . * gcc-13.patch: fixed upstream by different change….

Ethics statement All mice procedures in this study were performed under an animal protocol approved by the Institutional Animal Care and Use Committee guidelines of Westlake University. The procedures and protocols for glioma patients were approved by the institutional review board of Beijing Tiantan Hospital. Informed consent was obtained from…

I need to get a fasta sequence of a certain gene for a certain worm strain that is different from reference. I have a reference genome, BAM for the strain of interest, and coordinates of the gene. I know that vcftools can convert bam to fasta, but I do not…

This study is aimed at revealing the transgenerational effects of thia. We chose the developmental window from embryonic days 6.5 to E15.5 because of its importance in germ cell program establishment. The mice breeding was described in the Materials and Methods section “Mouse treatment and dissection.” The design of the…

Subjects The study was conducted in accordance with the Declaration of Helsinki and all subjects or their parents/guardian gave informed written consent for genetic testing. DNA testing and storage in the Beta Cell Research Bank was approved by the Wales Research Ethics Committee 5 Bangor (REC 17/WA/0327, IRAS project ID…

Bedtools coverage -hist “all” in chr column 0 $ bedtools coverage -a A.bed -b B.bed -hist chr1 0 100 b1 1 + 0 70 100 0.7000000 chr1 0 100 b1 1 + 1 30 100 0.3000000 chr1 100 200 b2 1 – 1 100 100 1.0000000 chr2 0 100 b3…

Abberton M, Batley J, Bentley A, Bryant J, Cai H, Cockram J, Costa de Oliveira A, Cseke LJ, Dempewolf H, De Pace C, Edwards D, Gepts P, Greenland A, Hall AE, Henry R, Hori K, Howe GT, Hughes S, Humphreys M, Lightfoot D, Marshall A, Mayes S, Nguyen HT, Ogbonnaya…

Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…

Hi I have two input files A BAM file A BED file I want to get an output of read counts for the regions specified in the BED file as JSON I have earlier used FeatureCounts for getting the read counts but there I used gtf and aligned BAM file…

De novo genome assemblies and genome annotation We assembled a de novo genome of a seven-year-old male SED from Ubon Ratchathani Zoo using a combination of Illumina short-reads (92.94 × coverage) and PacBio long-reads (61.6 × coverage) (GenBank accession number: JACCHN000000000). Additionally, we used MGI short-reads (52.15 × coverage) to assemble a de novo genome of…

Alternatives to snpflip to find ambigious and flipped snps 0 Hello everyone, I having an issue with strand flips when trying to perform imputation. In the past on an old HPC I used it supported snpflip, a tool which would recognize ambigious snps as well as snps that have been…

Researchers in molecular biology and computational biology need bioinformatics libraries. They offer many tools to understand biological information.  Scientists can focus on their research because these libraries simplify complicated computational tasks. Let’s delve into the world of bioinformatics libraries and explore their significance.       A bioinformatics library is a collection of…

Adrian1 November 12, 2023, 10:30pm 1 tool: bedgraph-to-bigwig input: bedgraph files from MACS2 output problem: result bigwig file has 0 lines tool standard output: hashMustFindVal: ‘GL456210.1’ not foundtool standard error” grep: write error: Broken pipe Error running wigToBigWig. more details: I used mm39 as the database/build for all my inputs,…

Filter a BED file based on genome coordinates for gene names 0 Hi, I have BED file with certain regions of interests that looks like this: chr1 0 91923 chr1 323234 4596845 … with the start and end coordinates for each gene for the respective chromosome. But I want to…

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

Hailey Bieber is the undeniable queen of sheen. Whenever she shares her beauty routine on social media, it’s always full of glow-inducing products, like the Peptide Glazing Fluid from her skin care line, Rhode. But one of her videos on TikTok also revealed a high-tech facial tool that seemed to…