Tag: snp

Popcorn using SNPs with extremely low P-value 0 I would like to use Popcorn to assess genetic corrleation between different populations. However, the summary statistics for one population contains a very small P-value, such as P-value=5.0×10^-1200. Perhaps that is why I cannot calculate the genetic correlation including this summary statistics….

BioResource biobanking We extract DNA from blood or saliva donated by our participants. The DNA is quality controlled, banked  and then analysed to study genetic variation by genotyping. We also store plasma and serum from blood samples. All samples are sent to the NIHR-funded National Biosample Centre (NBC) in Milton Keynes, for processing,…

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct. ggplot2 is a well-known data visualization package to use in R. As ggplot2 is well developed from the beginning, engineers can spend more…

Digeneans are one of the most unique and the most numerous groups of parasitic Platyhelminthes. Their life cycle is complex, with few parthenogenetic and a single hermaphroditic generation [21]. Due to the complexity of the life cycle, these parasites are frequently subject to various modifications to their life strategies. There…

LONDON, June 06, 2023 (GLOBE NEWSWIRE) — The newest report from Data Bridge Market Research, “Third Generation Sequencing Market” examines growth strategies, drivers, opportunities, key segments, Porter’s Five Forces analysis, and the competitive environment in detail. In order to thrive in the rapidly evolving marketplace, businesses today require innovative and…

NEW YORK – Molecular diagnostics startup Circular Genomics sees a more direct way to predict patient response to psychiatric medications by analyzing circular RNA (circRNA) molecules that brain cells shed into the bloodstream. The University of New Mexico spinout is focusing its efforts first on major depressive disorder (MDD), then…

Study design and participants The GCKD study is an ongoing prospective observational study that enrolled 5,217 adult persons with CKD between 2010 and 2012. Patients regularly seen by nephrologists with eGFR between 30 and 60 ml min−1 per 1.73 m2 or eGFR >60 ml min−1 per 1.73 m2 with UACR > 300 mg per g (or urinary protein/creatinine ratio > 500 mg…

We are seeking a Bioinformatics Scientist to join the team at the National Institutes of Heath’s Center for Immuno-Oncology (CIO). This is a Federal Government Contractor position and the candidate must be able to pass a background check. Responsibilities: Perform computational analysis, integration, and modeling of diverse data sets, to…

Introduction The definition of an individual organism, traditionally defined by the invariable presence of a physiological unit and genetic homogeneity, is challenged by situations such as intraorganismal genetic heterogeneity (IGH), which refers to the presence of more than one genotype in a single organism (Schweinsberg et al., 2015). Cells within a…

CNNScoreVariants Error 0 Hello guys, I have a problem with CNNScoreVariants code. When I use the code : gatk CNNScoreVariants \ -V input.vcf \ -R reference.fasta \ -O annotated.vcf It has given the error : !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! Warning: CNNScoreVariants is an EXPERIMENTAL tool and should not be used for production !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!…

Natera%2C+Inc. (NASDAQ: NTRA), a global leader in cell-free DNA testing, today announced new data on its Prospera test being presented at the American Transplant Congress (ATC) 2023 taking place June 3-7, 2023. The presentations include several interim analyses from ProActive, a prospective donor-derived cell-free DNA (dd-cfDNA) study evaluating Natera’s Prospera…

Oosthuizen T, Howes LM (2022) The development of forensic DNA analysis: new debates on the issue of fundamental human rights. Forensic Sci Int Genet 56:102606 Article  CAS  PubMed  Google Scholar  Nwawuba Stanley U et al (2020) Forensic DNA profiling: autosomal short tandem repeat as a prominent marker in crime investigation….

Thanks, Ann. Once again I started typing a reply, got distracted by, uh, events (Look! A squirrel!) and didn’t move the text over and check the thread before stabbing the “Add comment” button. As to RSRS and rCRS for the haplotree, I was primarily going by the fact that Mannis…

. 2023 May 17;10:1086001. doi: 10.3389/fvets.2023.1086001. eCollection 2023. Gianluigi Rossi  1   2 , Barbara Bo-Ju Shih  1 , Nkongho Franklyn Egbe  3 , Paolo Motta  4 , Florian Duchatel  1 , Robert Francis Kelly  5 , Lucy Ndip  6   7 , Melissa Sander  8 , Vincent Ngwang Tanya  9 , Samantha J Lycett  1   2 , Barend…

Upgrade In Progress:  EvE Premium is unavailable during the upgrade process. The new, upgraded version is scheduled for release in May 2023. Create Your Own Bioinformatics Pipeline: Powerful and Easy-to-use. Design your own ultra-fast, cloud-based pipeline in seconds. Use defaults or define specific parameters. It’s your choice! Preprocessing ✯ Alignment & Mapping…

calculate p value and associated z score for snp-gene pair 0 Hello everyone, I have genotype file and gene expression file. I want to see whether three of my rsid in genotype file is associated with gene expression. I used matrixeqtl R package to generate p value and see whether…

Reporting MSY haplogroups in horse populations around the globe A previously-released fine-scale MSY HT topology23,24 provided the basis for the selection of 16 MSY diagnostic markers for major haplogroups (mjHGs) in modern horse breeds. Genotyping these markers helped to differentiate Przewalski’s horses’, as well as six non-Crown and three Crown…

The key difference between SNP and RFLP is that SNP, or Single Nucleotide Polymorphism, is a genomic variant at a single base position in the DNA, while RFLP, Restriction Fragment Length Polymorphism, is the difference in homologous DNA sequences that can be detected by the presence of fragments of different lengths after…

Dear community I’m currently trying to try a GWAS for case control study using PLINK using whole exome VCF files. I understand that I need to convert these VCF files into PLINK’s binary format (bed/bim/fam) before I can proceed with the GWAS. From my literature I have to manually create…

Metagenome-assembled bacterial genomes Out of the 42 ISS metagenomes submitted at NCBI, only PMA-treated metagenomes (n = 21) representing the viable/intact cells were used for generating bacterial MAGs. Characteristics of MAGs (n = 46) such as genome size (2.6 to 6.6 Mb), completeness, contamination percentage, the average mean coverage, number…

Introduction Next-generation sequencing (NGS) enables scientists to decipher the genome for a deeper understanding of biology. Proven Illumina sequencing by synthesis (SBS) chemistry combined with award-winning DRAGEN secondary analysis delivers whole-genome sequencing (WGS) data with outstanding accuracy.1,2 DRAGEN Multigenome (graph) further improves mapping accuracy in challenging regions by ~50%.1 Still,…

How GATK pipeline called a homozygeous alternate allele (1/1) although one copy is supported by 0 reads ? 1 I have annotated SNPs using GATK, and have observed that in many 1/1 SNP sites (homozygeous alternate) the whole read depth (stated in DP) are supporting the the alternate allele (as…

NEW YORK – As the venture capital market has cooled in the wake of rising interest rates, personalized health software company SelfDecode has “set aside” a planned new VC round and quietly raised a $2 million add-on to an earlier seed round, according to COO Ralph Kenney. The Miami-based firm…

PRSice-2 using SNPs with extremely low P-value 0 I would like to construct a Polygenic risk score using PRSice-2. However, our summary statistics contains a very small P-value, such as P-value=5.0×10^-1200. Perhaps that is why we cannot use this summary statistics to construct the PRS. How can I solve this…

how to look for interactions between different chromosomes 0 Hello everyone, I have a HiC data which has chromosomal interaction. But this dataset has chr20 region interacting with chr20 region. I want to look for datasets that have inter chromosomal interactions. like chr20 region interactin with chr2 region. Is there…

snpEff error. No CDS checked 0 I am building a database for genome annotation of dogs’ WES. I follow snpEff instructions from here My gtf, fasta, cds files are all from the same source here However, in Step 3 (checking database) I get an error that transcript IDs from the…

Hunt, T. et al. A comprehensive phylogeny of beetles reveals the evolutionary origins of a superradiation. Science 318, 1913–1916 (2007). Article  ADS  CAS  PubMed  Google Scholar  Crowson, R. A. The phylogeny of coleoptera. Annu. Rev. Entomol. 5, 111–134 (1960). Article  Google Scholar  Darwin, C. The Descent of Man, and Selection…

DOI: 10.18129/B9.bioc.gpart     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see gpart. Human genome partitioning of dense sequencing data by identifying haplotype blocks Bioconductor version: 3.13 we provide a new SNP sequence partitioning method which partitions the whole SNP sequence based on…

Hello, I am calculating PRSs using the command:  plink2 \–bfile plink_file \–score score_file 1 2 3 header cols=+scoresums,-scoreavgs \–out PRS_sum Currently,  the columns in my score_file are: SNP IDs, effect allele, beta weights. I was wondering if possible to give instead of SNP IDs in the first column, chrs and…

Transcribed image text: Restriction Digestion Planning for RFLP Q5. What are restriction enzymes and recognition sites? What is their function in nature? How can a mutation alter a recognition site? [10pts] Q6. Appendix I shows the restriction sites for NEB enzymes for the complete PTC gene. Choose a restriction enzyme…

Vogel, B. et al. The Lancet women and cardiovascular disease Commission: reducing the global burden by 2030. Lancet 397, 2385–2438 (2021). Article  PubMed  Google Scholar  Adlam, D., Alfonso, F., Maas, A., Vrints, C. & Writing Committee. European Society of Cardiology, acute cardiovascular care association, SCAD study group: a position paper…

GBD 2016 Disease Injury Incidence Prevalence Collaborators. Global, regional, and national incidence, prevalence, and years lived with disability for 328 diseases and injuries for 195 countries, 1990-2016: a systematic analysis for the Global Burden of Disease Study 2016. Lancet. 2017;390:1211–59. Article  Google Scholar  Kato T. Current understanding of bipolar disorder:…

Badouin H, Gouzy J, Grassa CJ, Murat F, Staton SE et al (2017) The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution. Nature 546:148–152 Article  CAS  PubMed  Google Scholar  Gilley MA, Gulya TJ, Seiler GJ, Underwood W, Hulke BS, Misar CG, Markell SG (2020) Determination of virulence…

Brief overview of inference approach Mutations occur during viral replication within infected individuals and these have the potential to be transmitted. During the epidemiological spread of an emerging virus or viral lineage, the virus population (distributed across infected individuals) thus accrues mutations and diversifies genetically. This joint process of viral…

Merging multiple PLINK files 0 Hello, I’ve been trying to merge multiple PLINK files (bed bim fam). I have 6 datasets that are genotyped on different genotyping arrays. So technically when I try to merge them using the command plink –bfile dataset1 –merge-list all_lists.txt –make-bed –out merged_data I get multiple…

NEW YORK, May 29, 2023 (GLOBE NEWSWIRE) — Data Bridge Market Research has unveiled a new report called “Gene synthesis software Market” which provides an in-depth exploration of growth strategies, drivers, opportunities, key segments, Porter’s Five Forces analysis, and the competitive landscape. Globalization makes it clear that market research report…

Liu, L. et al. Identification of quantitative trait loci for growth-related traits in the swimming crab Portunus trituberculatus. Aquacult. Res. 46, 850–860 (2015). Article  CAS  Google Scholar  Sun, Q. F. et al. Astaxanthin: The ubiquitous and abundant carotenoid as a pivotal interior factor of anti-oxidation and immune for the moulting…

I am seeing a 5-10% reduction in reads mapped to a genome graph compared to a linear reference of the same genome sequence. I have two graphs: one is the reference genome decorated with 5 million SNPs and the other is an empty graph created with vg using the reference…

Description of the workplaceThe Cardiovascular research – Translational studies is studying cardiovascular disease with a focus on biological differences that underlie acute complications such as heart attacks and strokes. The research is translational and includes studies of human tissue and several in-vitro models. The group has for many years been…

How extract specific SNP position from the bed file-Bedtools 1 I have one bed file with start and end coordinate (range in bed format). I need to extract a specific position from this range bed (for example I need to extract “chr12 25392999” position from the below bed file). How…

A major expansion of the Applied Genomics Centre (AGC) at Kwantlen Polytechnic University’s (KPU) Surrey campus and the new funding will improve research and further expand opportunities for students. Andrew Mercier, B.C. Minister of State for Workforce Development, and Sukh Dhaliwal, MP for Surrey-Newton, joined KPU President and Vice-Chancellor Dr….

Bessant, D. A., Ali, R. R. & Bhattacharya, S. S. Molecular genetics and prospects for therapy of the inherited retinal dystrophies. Curr. Opin. Genet. Dev. 11, 307–316 (2001). Article  CAS  PubMed  Google Scholar  Berger, W., Kloeckener-Gruissem, B. & Neidhardt, J. The molecular basis of human retinal and vitreoretinal diseases. Prog….

Transcribed image text: 1. Hair without the root can most likely yield what genetic information? genomic SNP data STR profile mtDNA sequence none of these Y-STR profile Which of the following would be least useful in discriminating male siblings with a different mother but same father from one another? Autosomal…

We analyzed data from a total of 2,733 participants from the GALA II16 and SAGE17 asthma case–control studies who self-identified as African American (AA; n = 757), Puerto Rican (PR; n = 893), Mexican American (MX; n = 784) or other Latino American (LA; n = 299) (Table 1 and Supplementary Table 1). The median age of the…

The UKB is approved by the North West Multi-centre Research Ethics Committee (www.ukbiobank.ac.uk/learn-more-about-uk-biobank/about-us/ethics). The current study was conducted under UKB application no. 26041. The data in the UKB were collected after written informed consent was obtained from all participants. The Human Research Committee of the MGB approved the Biobank research…

Kiu, R. & Hall, L. J. An update on the human and animal enteric pathogen Clostridium perfringens. Emerg. Microbes Infect. 7, 141 (2018). Article  PubMed  PubMed Central  Google Scholar  Li, J., Paredes-Sabja, D., Sarker, M. R. & McClane, B. A. Clostridium perfringens sporulation and sporulation-associated toxin production. Microbiol. Spectr. doi.org/10.1128/microbiolspec.TBS-0022-2015…

Variant calling in WES vs WGS 2 I used SnpEff tool to annotate variants in whole exome sequencing data. However, most variants in the results came out as intron and intergenic variant types. What can be the reason behind it? I couldn’t find a specific command for WES data in…

The infant and maternal gut microbiota are defined by different Bifidobacterium species The samples analysed in this study were collected during the MicrobeMom study (ISRCTN5302301420,21), these included samples from the maternal stool, vagina, oral cavity, and breast milk in addition to infant stool (Table 1; Fig. 1a). From the 160 participants recruited,…

how to run FacetsSuite wrapper scripts on command line 0 Hi, I am very new to using FACETS. I was wondering if there is a way to run the Rscript snp-pile-wrapper.R directly on the command line without installing facets using conda or from GitHub. Is this possible? I’ve tried running…

For a paper appearing in Cell Genomics, a University of Witwatersrand-led team compares genotype imputation across five reference panels comprised of roughly 10,900 samples from sub-Saharan African (SSA) populations. As part of the “Africa-Wits INDEPTH Partnership for Genomics Studies in African populations,” or AWI-Gen, study, the team imputed data from…

Ahmad L, Eshlaghy A, Poorebrahimi A, Ebrahimi M, Razavi A (2013) Using three machine learning techniques for predicting breast cancer recurrence. J Health Med Inform 4(124):3 Google Scholar  Bochare A, Gangopadhyay A, Yesha Y, Joshi A, Yesha Y, Brady M, Grasso MA, Rishe N (2014) Integrating domain knowledge in supervised…

Lund University, Faculty of Medicine, Department of Clinical Sciences, Malmö Description of the workplaceThe Cardiovascular research – Translational studies is studying cardiovascular disease with a focus on biological differences that underlie acute complications such as heart attacks and strokes. The research is translational and includes studies of human tissue and…

Aase K, Jensen H, Muff S (2022) Genomic estimation of quantitative genetic parameters in wild admixed populations. Meth Ecol Evol 13:1014–1026 Article  Google Scholar  Aitken SN, Bemmels JB (2015) Time to get moving: Assisted gene flow of forest trees. Evol Appl 9:271–290 Article  PubMed  PubMed Central  Google Scholar  Alberto F…

Transcribed image text: Instructions Associated questions refer to a gene in the human genome. The screenshot below should help you find the location of the gene in the human genome (hg38). Navigate to this gene in the UCSC Genome Browser (not GEP mirror site) to answer attached questions. Epo-last exon…

Retrieving information from COSMIC database in an automated way 0 Hi! I am performing variant calling and annotation of some cancer samples. For the moment, I am checking manually the variants with an entry in the COSMIC database and then going to the COSMIC database website to retrieve information associated…

Allele frequency visualization 2 Hello dears all, Actually I have a .frq file (allele frequency file) which It is generated from .vcf file through VCFtools and it is included by five populations (The vcf file is generated by Stacks pipeline). But the point is, I don’t know how can I…

Hi-Throughput DNA Isolation LGC oKtopure The oKtopure™ is a fully automated nucleic acid extraction platform that combines high-throughput automation with the proprietary sbeadex™ magnetic bead based extraction chemistry for high quality, high yield extraction. Key to the delivery of consistently high quality and high yield DNA preparations from the oKtopure…

Background: To reduce the cost of genomic selection, a low-density (LD) single nucleotide polymorphism (SNP) chip can be used in combination with imputation for genotyping selection candidates instead of using a high-density (HD) SNP chip. Next-generation sequencing (NGS) techniques have been increasingly used in livestock species but remain expensive for…

NEW YORK – New genetic research is providing demographic insights into the early colonial settlement of the US East Coast — from ancestry that resembled populations in northwestern Europe to enslaved individuals from different parts of Africa. Such results “are contributing to a growing body of evidence from colonial era…

Molecular profiling reveals common changes in matched pairs of HNSCC primary tumor and metastasis-derived cell lines Identification of both genetic and functional differences between primary and metastatic variants of HNSCC would be enabled by in vitro models derived independently from these sites from the same patient. Unfortunately, HNSCC tumor cells…

Introduction Tuberculosis (TB), caused by Mycobacterium tuberculosis, is one of the leading causes of death worldwide and caused 1.6 million deaths and 10.6 million new cases in 2021.1 Despite decades of efforts to adopt measures to control TB, achieving the goal of ending TB has been delayed due to a…

Significance of “orientation” flag in FilterMutectCalls output 0 Hi! I have an annotated vcf file generated by mutect2 and flagged by FliterMutectCalls. Thing is, I have found my variant of interest but it is not flagged as PASS but as “orientation”. I want to know if the read orientation bias…

Converting Microarray SNP data into VCF format 1 Hello everyone, I have only one microarray data which contains one .CEL file and another intensity .csv file. I’m searching for converting any of the two files into vcf format. After going through Biostars and Bioconductor forums, I found pd.genomewidesnp.6@getdb, crlmm and…

Introduction Multidrug-resistant Enterobacteriaceae infection is a severe threat to public health that is worsening globally and is associated with increasing mortality rates.1 Klebsiella pneumoniae is a significant pathogen that contributes to the dissemination of multidrug-resistant strains in healthcare environments.2 K. michiganensis is a novel specie of pathogenic Klebsiella genus. Since…

DOI: 10.18129/B9.bioc.SNPlocs.Hsapiens.dbSNP149.GRCh38     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see SNPlocs.Hsapiens.dbSNP149.GRCh38. SNP locations for Homo sapiens (dbSNP Build 149) Bioconductor version: 3.15 SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for…

1. Introduction Lactococcosis is a serious septicemic fish disease in Mediterranean countries. Lactococcus garvieae was considered the sole causative agent of lactococcosis until recently. L. garvieae has been isolated as a causative agent of the disease in several freshwater and marine species such as rainbow trout (Oncorhynchus mykiss), tilapia (Oreochromis…

The domestic canary (Serinus canaria) is one of the most common pet birds and has been extensively selected and bred over the last few centuries to constitute many different varieties. Plumage pigmentation is one of the main phenotypic traits that distinguish canary breeds and lines. Feather colours in these birds,…

Image by Frohe Weihnachten Research into equine herpesvirus (EHV) has received a major boost with funding for two projects from the Grayson-Jockey Club Research Foundation. Equine herpesvirus (EHV-1) and Equid Herpesvirus Myeloencephalopathy (EHM) are highly contagious, affecting horses of every breed and discipline, and they continue to cause significant economic…

Osteoarthritis is a degenerative disease that is influenced by multiple factors, such as age, BMI, sex, mechanical abnormalities, previous injury, and genetics11. Recently, more studies have focused on the relationship between genetic polymorphisms and osteoarthritis. This is the first case–control study to be performed in Indonesia that focuses on the…

SnpEff Error 1 Hello guys, I. run this code : snpEff Prunus_armeniaca_cv_Stella.gff3.gz output.vcf > output.txt I am getting this Error! Could you pls help me with this issue? java.lang.RuntimeException: Property: ‘Prunus_armeniaca_cv_Stella.gff3.gz.genome’ not found at org.snpeff.interval.Genome.<init>(Genome.java:104) at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:784) at org.snpeff.snpEffect.Config.readConfig(Config.java:751) at org.snpeff.snpEffect.Config.init(Config.java:529) at org.snpeff.snpEffect.Config.<init>(Config.java:116) at org.snpeff.SnpEff.loadConfig(SnpEff.java:429) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875) at…

Acclimatisation (6 January 1877) Southland Times. Page 2. paperspast.natlib.govt.nz/newspapers/ST18770105.2.7. Accessed 21 January 2022 Adamack AT, Gruber B (2014) PopGenReport: simplifying basic population genetic analyses in R. Methods Ecol Evol 5:384–387. doi.org/10.1111/2041-210x.12158 Article  Google Scholar  Andrews S (2010) FastQC. A quality control tool for high throughput sequence data. www.bioinformatics.babraham.ac.uk/projects/fastqc/ Andrews KR,…

Data collection for HRD prediction model training and validation For the development of the HRD prediction model, 1854 samples (WGS data) from the pan-cancer analysis of whole genomes9 (PCAWG) and 560 breast cancer samples (SNP array data)16 are collected. To obtain a high-confidence training dataset of HRD, samples with BRCA1/2…

1. Introduction Shiga toxin-producing Escherichia coli (STEC) is a Gram-negative foodborne pathogen that was estimated to cause ~265,000 infections, 3600 hospitalizations, and 30 deaths in the U.S. each year [1]. Most patients with STEC infections develop diarrhea and abdominal pain, though hemolytic uremic syndrome (HUS) and kidney failure can occur,…

It is definitely possible to assess paternity from whole genome sequence (WGS) data. Paternity can probably be established with as little as a few dozen or maybe hundreds of well-chosen single nucleotide polymorphisms (SNPs). If you have decent WGS data you can expect to genotype millions of SNPs. So, paternity…

This study is led by Dr. Shouchuang Wang (Sanya Nanfan Research Institute of Hainan University), revealing the role of epigenetic variation in tomato domestication and metabolic diversity from the perspective of population DNA methylation. The breeding history of tomato which is a world recognized model plant with high nutritional value…

Introduction The yield of genetic prenatal diagnosis has been notably improved by introducing whole genome chromosomal microarray (CMA) analysis, which is now recommended in all cases with structural anomalies,1 allowing an additional diagnostic yield as compared to karyotyping of up to 10%.2,3 Moreover, recent data suggest that the expected diagnostic…

Difference between variants called in sequences with 2-channel SBS and 4-channel SBS 0 Hi all. I have been using 4-channel SBS for sample sequencing and am considering using 2-channel SBS in the future. I would like to know if there are any papers that discuss the differences in SNPs obtained…

Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013). Article  CAS …

Hello, I am trying to do something very simple, but running into confusing behaviour. I have a VCF file of multiple samples and want to remove all indels so that I can generate sequences with identical coordinates with bcftools consensus. I removed indels by specifying bcftools view –include ‘TYPE=”snp” ||…

How to extract regions from BAM file on remote server and visualize long-read alignments in IGV? 1 Hello, I have code that indicates there are a number of SNP mutations at specific locations for different cell types and none for others. I need to align all the respective longreads at…

1. Introduction 2. Basic information 3. Downloads and general notes 4. Command reference table 5. Basic usage/data formats 6. Data management 7. Summary stats 8. Inclusion trim 9. Population stratification 10. IBS/IBD estimation 11. Bond 12. Family-based community 13. Permutation process 14. LD calculations 15. Multimarker tests 16. Conditional haplotype…

The mitochondrial genome structure of mollusks shows a high degree of variability involving many genomic features, i.e., length, gene arrangement, strand assignment, gene duplication and loss, nucleotide composition, etc. It shows extensive variation in mollusks, gastropods, and bivalves, even within the same family or genus. Mitochondrial DNA (mtDNA) has been…

Genotyping Market Genotyping Market Report Scope and Research Methodology The report provides a holistic view of the market by integrating qualitative and quantitative data. The data was collected through primary and secondary research methods, including surveys, interviews with key industry players, and data analysis of reputable sources. For detail insights…

Animal rearing and samples collection Our experiment was designed to compare eight female Laiwu pigs (LW) with eight female Lulai pigs (LU) which crossbred between LW and Yorkshire breeds. All pigs were born and raised for approximately two years (715 ± 33 days, Table 1) under uniform housing and feeding conditions at Jing-Qi-Shen…

Job Family: Data Science & Analysis Travel Required: None Clearance Required: Ability to Obtain Public Trust What You Will Do: Perform computational analysis, integration, and modeling of diverse data sets, to include microarray, bulk and single-cell RNAseq, ATAC-seq, flow and CyTOF phenotyping, serum proteome, SNP genotyping, and microbiome profiling Perform…

Job Family: Data Science & Analysis Travel Required: None Clearance Required: Ability to Obtain Public Trust What You Will Do: Perform computational analysis, integration, and modeling of diverse data sets, to include microarray, bulk and single-cell RNAseq, ATAC-seq, flow and CyTOF phenotyping, serum proteome, SNP genotyping, and microbiome profiling Perform…

Somatic variant calling mutect2 ctDNA liquid biopsy 0 Hi! I am trying to call ctDNA somatic variants in a sample that comes from liquid biopsy of a cancer patient. I also have a healthy control that comes from an in-house plasma sample. I want to apply mutect2 but I have…

Hi there, I have two separate sets of gwas data (‘A’ and ‘B’) with a file per chr.  I am running a targeted gene/pathway analysis so I have filtered out snps per each gene location (209 snps = 209 filtered gene-specific files). For dataset A I ran the following commands:…

Schistosomiasis is a disease of global medical and veterinary importance, caused by parasitic flatworms of the genus Schistosoma. Around 200 million people, and an untold number (possibly in the billions) of animals are estimated to be infected, globally. Certain schistosome species can infect humans (e.g. Schistosoma mansoni and S. haematobium),…

Transcribed image text: There is a new RFLP locus identified for Brassica rapa named Park13. Below are the two possible alleles for this locus: SnpT and SnpS. Both alleles are the same total length (1200 bp:1). but they have different restriction enzyme cut sites when digested with BamHI. You will…

KING kinship inference error 2 Hello, I’m trying to use KING for estimating kinship between individuals. I have a vcf file that resulted from a de novo assembly of ddrad seq data. First, I tried to convert my vcf file to .bed file using Plink2.0, but it failed saying that…

Sample based on allele frequency matching between two files 0 I have two files, each of which has the SNP_ID and its allele frequency. File 1 has a set of 200 SNPs (subset from my genome) and their respective allele frequencies, whereas File 2 is every SNP in the genome…

Good afternoon! It’s great to see you getting into bioinformatics. I can definitely help you get started with your linkage disequilibrium (LD) analysis using Plink. Here’s a general workflow to perform LD analysis using Plink with your Saccharomyces cerevisiae samples: First, you need to install Plink if you haven’t already….

How to find DNA sequence of a SNP without reference genome? (I have a .vcf file) 0 Hi. I have a “VCF” file that i’ve created “de novo”. That is, I have NOT mapped my reads to a reference genome, but rather constructed this VCF by utilizing sequence similarity. Within…

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, and was edited by Istvan…

Transcribed image text: The K-ras gene produces an important signaling peptide that leads to cell cycle induction. It is a proto-oncogene and dominant gain of function mutations can lead to cancer. The gene is found on chromosome 12 in humans and the wild type form has two palindromic sequences reco…

Hi, I use a loop for that. Something like this to inspire you: # Enter folder where gnomAD data are here: gnomAD=”/path/to/gnomAD/database/release/3.1.2/gnomad.genomes.v3.1.2.sites.” # Enter the folder where your results are and will be annotated further cd /path/to/your/results/folder/ # Enter the name of the final results’ file from SnpSift ann=”results.ann.gnomAD.genomes.v3.1.2.vcf” #…

Report Description: The Gene Amplification Technologies Market 2023 research report appears to cover various aspects of the market, including the strategies of top players, market segments, competitive landscape, manufacturing, and pricing structures.  In this report, we will provide an in-depth analysis of the current state of the global Gene Amplification…

I have recently found some variants which appear in Clinvar searching by coordinate but not by their RS ID. ID: rs111254723 Clinvar: www.ncbi.nlm.nih.gov/clinvar/variation/2445388/ dbSNP: www.ncbi.nlm.nih.gov/snp/rs111254723#clinical_significance This is an example of one of them. The same variant appears in dbSNP searching by its RS identifier, but its clinical significance field is…

Using a transcriptome from Trinity in Phyluce 0 Hi there, I’m working with multiple RNA seq samples. These samples belong to bird blood infected with malaria parasites. The genome reference for the parasite species is not available. Most of my reads belong to bird and I’m not interesting on them…only…