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Tag: Varscan
Arsenic is a potent co-mutagen of ultraviolet light
Barnes, J. L., Zubair, M., John, K., Poirier, M. C. & Martin, F. L. Carcinogens and DNA damage. Biochem. Soc. Trans. 46, 1213–1224 (2018). Article CAS PubMed PubMed Central Google Scholar Ames, B. N., Durston, W. E., Yamasaki, E. & Lee, F. D. Carcinogens are mutagens: a simple test system…
Whole mitochondrial and chloroplast genome sequencing of Tunisian date palm cultivars: diversity and evolutionary relationships | BMC Genomics
Johnson DV, Al-Khayri JM, Jain SM. Introduction: Date Production Status and Prospects in Africa and the Americas. In: Al-Khayri J, Jain S, Johnson D, editors. Date Palm Genetic Resources and Utilization: Volume 1: Africa and the Americas. Springer Netherlands, Dordrecht; 2015. p. 1–18. doi.org/10.1007/978-94-017-9694-1_1 Gros-Balthazard M, Hazzouri KM, Flowers JM. Genomic…
Transition of allele-specific DNA hydroxymethylation at regulatory loci is associated with phenotypic variation in monozygotic twins discordant for psychiatric disorders | BMC Medicine
Lichtenstein P, Yip BH, Bjork C, Pawitan Y, Cannon TD, Sullivan PF, Hultman CM. Common genetic determinants of schizophrenia and bipolar disorder in Swedish families: a population-based study. Lancet. 2009;373(9659):234–9. Article PubMed Google Scholar Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Wang H, Reynolds AP, Sandstrom R,…
Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing
Tsudzuki, M. Mutations of Japanese quail (Coturnix japonica) and recent advances of molecular genetics for this species. J. Poult. Sci. 45, 159–179 (2008). CAS Google Scholar Recoquillay, J. et al. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genom. 16, 10 (2015)….
Detecting somatic variants in non-tumor tissue without normals
I’m new to genome analysis, so apologies if this is a basic question. My hypothesis is that in a particular disease, gene XYZ contains somatic mutations. I have performed targeted sequencing of gene XYZ with very high coverage using Sureselect. I have sequenced the gene in brain tissue from diseased…
Characterization of the genomic alterations in poorly differentiated thyroid cancer
Cancer Genome Atlas Research, N. Integrated genomic characterization of papillary thyroid carcinoma. Cell 159, 676–690. doi.org/10.1016/j.cell.2014.09.050 (2014). Sherman, S. I. Thyroid carcinoma. Lancet 361, 501–511. doi.org/10.1016/s0140-6736(03)12488-9 (2003). Article PubMed Google Scholar Tong, J. et al. Poorly differentiated thyroid carcinoma: a clinician’s perspective. Eur. Thyroid J. 11, doi.org/10.1530/ETJ-22-0021 (2022). Asioli, S….
How to interpret the Variant Allele Frequency??
How to interpret the Variant Allele Frequency?? 0 I am new to the field of Bioinformatics and seeking guidance. I am currently in the process of calculating the Variant Allele Frequency (VAF) using the VarScan software. I have obtained the results and have included screenshots for reference. I would greatly…
Guide to Quality Control for Viral Sequencing
Viral sequencing has evolved into a sophisticated tool, empowering researchers to unravel the intricacies of viral genomes and their implications on human health. As we delve into the realm of viral genomics, meticulous quality control (QC) steps become indispensable to ensure the fidelity and accuracy of sequencing data. In this…
Whole genome sequencing of drug resistance Mycobacterium tuberculosis from extra-pulmonary sites
Introduction Tuberculosis is a threat to human health caused by Mycobacterium tuberculosis that affected lung and other extra-pulmonary sites. There was an estimated 10.0 million people fell ill with TB, 1.2 million TB deaths among HIV-negative people, and an additional 251,000 deaths among HIV-positive people in 2018 (World Health Organization,…
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE? 2 Hey namhaesly, You need to create segmentation files for your data. You can use VarScan2 (the copynumber) function, or any other program that computes copy number information. My tool of choice is ExomeCNV though I don’t…
How to read Varscan VCF output in column “Cons”?
How to read Varscan VCF output in column “Cons”? 0 Hi, I am trying to use Varscan2 to make indel calls from pileup files created by samtools. The process ran very smooth but I got confused with the output. I don’t know how to read the result of the indel….
open-cravat: variant annotation tool
Tool:open-cravat: variant annotation tool 3 open-cravat is an open-source platform for rapidly developing, using, and disseminating variant annotation tools. It can handle unlimited number of variants in VCF format input files as well as its own input format and produce tab-separated text output files and excel spreadsheets. It is command-line-based…
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files 0 Leung et al., 2017 paper mentioned in Fig 1 data processing for CRC patients was sequenced as single cell for both SNV (with MDA WGA) and CNA (with DOP-PCR) parallelly….
Soniazid and ethionamide in Mycobacterium tuberculosis
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…
cfsan snp pipeline
cfsan snp pipeline 1 I am using cfsan_snp_pipeline. The link of the git is- I have installed all the dependencies and install the pipeline via conda. when I execute the command- echo $CLASSPATH /home/saiful/home/saiful/Downloads/picard-2.18.2.jar:/home/saiful/home/saiful/Downloads/VarScan.v2.3.9.jar:/home/saiful/home/saiful/Downloads/GenomeAnalysisTK-3.8-1/GenomeAnalysisTK.jar: when I run the pipeline, cfsan_snp_pipeline run genomic.fasta -o cfsan_pipeline -s listeria Checking dependencies… CLASSPATH is…
How to plot venn diagram from vcf-compare output ?
How to plot venn diagram from vcf-compare output ? 1 i get the following output from vcf-compare by comparing two VCF : VN 2172 NA12878/intersect2.vcf.gz (6.8%) VN 29648 Coriell.varscan.snp.vcf.gz (20.7%) NA12878/intersect2.vcf.gz (93.2%) VN 113680 Coriell.varscan.snp.vcf.gz (79.3%) I would like to plot a Venn diagram quickly. Any idea ? Online tool…
ABSOLUTE for tumour purity with WES
ABSOLUTE for tumour purity with WES 0 Hello, I have WES paired data (tumour and normal) from Illumina sequencing and I would like to obtain a purity score. ABSOLUTE seemed perfect but I can’t get it to work. Here’s my workflow: Generate .pileup from .bam with SamTools Generate .copynumber from…
Genetic sequencing of a 1944 Rocky Mountain spotted fever vaccine
Harden, V. A. Rocky mountain spotted fever: History of a twentieth-century disease Vol. 16 (Johns Hopkins University Press, 1990). Google Scholar Maxey, E. E. M., G T; Leary, J W. (1899) Some observations on the so-called spotted fever of Idaho. Med Sentinel, 7: 433–438. Dantas-Torres, F. Rocky mountain spotted fever….
Neoantigen-targeted CD8+ T cell responses with PD-1 blockade therapy
Schumacher, T. N. & Schreiber, R. D. Neoantigens in cancer immunotherapy. Science 348, 69–74 (2015). Article ADS CAS PubMed Google Scholar Tran, E., Robbins, P. F. & Rosenberg, S. A. Final common pathway’ of human cancer immunotherapy: targeting random somatic mutations. Nat. Immunol. 18, 255–262 (2017). Article CAS PubMed PubMed…
Obtaining bcf and vcf files and use bcf tool annotate
Obtaining bcf and vcf files and use bcf tool annotate 1 I have vcf file that I obtained from the galaxy and I want to run bcftools annotate. I ran the following command: bcftools annotate -a Galaxy96-\[Galaxy45-\[VarScan_on_data_44\].vcf\].vcf -o samtools_annotated.vcf But no output file is generated? How can I use different…
Powering Toxicogenomic Studies by Applying Machine Learning to Genomic Sequencing and Variant Detection
Alexandrov LB, Nik-Zainal S, Wedge DC et al (2013) Signatures of mutational processes in human cancer. Nature 500:415–421. doi.org/10.1038/nature12477 CrossRef CAS Google Scholar Alioto TS, Buchhalter I, Derdak S et al (2015) A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing. Nat Commun 6:10001. doi.org/10.1038/ncomms10001 CrossRef CAS …
In vivo hypermutation and continuous evolution
Arnold, F. H. Design by directed evolution. Acc. Chem. Res. 31, 125–131 (1998). Google Scholar Packer, M. S. & Liu, D. R. Methods for the directed evolution of proteins. Nat. Rev. Genet. 16, 379–394 (2015). Google Scholar Drake, J. W., Charlesworth, B., Charlesworth, D. & Crow, J. F. Rates of…
Failure to detect mutations in U2AF1 due to changes in the GRCh38 reference sequence
Materials and Methods Genomic data was collected as part of the MDS National History Study or The Cancer Genome Atlas project and consented appropriately under those protocols 8 Sekeres M.A. Gore S.D. Stablein D.M. DiFronzo N. Abel G.A. DeZern A.E. Troy J.D. Rollison D.E. Thomas J.W. Waclawiw M.A. Liu J.J….
The sardine run in southeastern Africa is a mass migration into an ecological trap
INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…
Assistant Research Professor – Genomics and Bioinformatics job with City of Hope
About City of Hope City of Hope, an innovative biomedical research, treatment and educational institution with over 6000 employees, is dedicated to the prevention and cure of cancer and other life-threatening diseases and guided by a compassionate, patient-centered philosophy. Founded in 1913 and headquartered in Duarte, California, City of Hope…