Tag: GSA
Idat raw data conversion
Idat raw data conversion 0 Hello everybody We have just started genotyping with GSA and generated first idat files. To QC we were advices to use GenomeStudio and for that we downloaded all the necessary files: bpm, egt, imap files from illumina website. Yet when we performed analysis in Genomestudio,…
what is the mean of the file “*._f1.fq.gz” and “*._r2.fa.gz”
what is the mean of the file “*._f1.fq.gz” and “*._r2.fa.gz” 1 Hello, I downloaded the files from: bigd.big.ac.cn/gsa/ The file is ended with: ” *._f1.fq.gz” and ” *._r2.fa.gz”. Is it single-end or paired-end sequencing? If it is paired-end sequencing, the file should be: ” *._r1.fq.gz” and ” *._r2.fa.gz”, not ”…
10X scRNA-seq v2 odd fastq format
10X scRNA-seq v2 odd fastq format 1 Hi Biostars, I’ve downloaded some scRNA-Seq data from the GSA, which I am hoping to analyze. This is 10x V2 chemistry sequence data. However the format is different from what I am familiar with. First, the reads come in 2 fastq files (“f1”…
Detecting drug resistance of Mycobacterium tuberculosis
Introduction According to the World Health Organization report 2022, the incidence rate of tuberculosis in China is 7.4%, with a year-on-year increase of 1.6%. China ranks third globally in terms of tuberculosis cases, with the top three countries being developing nations.1 It is worth noting that the tuberculosis mortality rate…
Effect of a microencapsulated probiotic on the intestinal microbiome of Pacific white shrimp
21 August 2023 Chung-Hung Liu Microencapsulation of Bacillus subtilis E20 proved effective in addressing probiotic issues related to inclusion during feed manufacturing Results of this study showed that microencapsulation was effective in addressing probiotic issues related to inclusion during feed manufacturing, that encapsulated B. subtilis E20 administration increased beneficial strains…
A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population
In the present study, we enrolled 412 participants from the Southeast Asian Brugada syndrome cohort (ClinicalTrials.gov number, NCT04232787). The study was approved by the Institutional Review Board (IRB) of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 431/58). All methods were performed in accordance with relevant guidelines/regulations. Informed…
Enrichment analysis on scRNSseq on which genes/clusters perform ReactomeGSA and GSEA?
Enrichment analysis on scRNSseq on which genes/clusters perform ReactomeGSA and GSEA? 0 Hi all, I have a question about gene ontology/GSEA and reactome analyses on scRNAseq dataset. I don’t understand on which genes/clusters is correct to perform these analyses? Do I have to perform these analysis on all clusters (post…
Creating a teleost fish traceability program based on genetic data from the Pacific coast of Panama
24 July 2023 Carlos Ramos-Delgado, Ph.D. A total of 34 species from 14 families were identified at the species level from 164 sequences This research provides important information and molecular tools for accurate identification of marine fish species in Panama and their traceability along the supply chain by providing species-specific…
Productions Manager job with UNIVERSITY OF SURREY
GSA Location: Guildford Salary: £35,308 to £43,155 Post Type: Full Time Closing Date: 23.59 hours BST on Sunday 13 August 2023 Reference: 032423 Guildford School of Acting at the University of Surrey is one of the most highly regarded conservatoires in the UK, with a vibrant community of performers, performance makers,…
Global DNA and Gene Chip Market to Reach USD 14.03 Billion by 2028, Fueled by Wide Application in Diverse Sectors
Reports And Data The Global DNA and Gene Chip Market is projected to grow at a CAGR of 11.4% from USD 5.84 Billion in 2020 to USD 14.03 Billion in 2028. NEW YORK CITY, NY, UNITED STATES, June 21, 2023/EINPresswire.com/ — The global DNA and Gene Chip Market is expected…
glm sample size vs OBS_CT
I am running glm with plink2. See code below: PLINK v2.00a3.6 AVX2 (14 Aug 2022) www.cog-genomics.org/plink/2.0/(C) 2005-2022 Shaun Purcell, Christopher Chang GNU General Public License v3Logging to /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/results/phthalates_mb/mecpp/mecpp.log.Options in effect: –bfile /PROJECTES/HELIX_OMICS/data_final/gwas/child/8y/GSA_QC3.HRCimp_20210615/HELIX.impQC.rs.05.EUR –covar /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/db/HELIX_phtalates_cov_plink.txt –covar-name PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8,…
protein abrupt-like isoform x1, maker-scaffold97_size377342-snap-gene-2.14 (gene) Tigriopus kingsejongensis
Associated RNAi Experiments Homology BLAST of protein abrupt-like isoform x1 vs. L. salmonis genes Match: EMLSAG00000011120 (supercontig:LSalAtl2s:LSalAtl2s753:207020:208693:1 gene:EMLSAG00000011120 transcript:EMLSAT00000011120 description:”augustus_masked-LSalAtl2s753-processed-gene-1.1″) HSP 1 Score: 342.043 bits (876), Expect = 1.286e-109Identity = 269/559 (48.12%), Postives = 311/559 (55.64%), Query Frame = 0 Query: 168 DNFGPSAPKRHRFNGPESRNSPSSSPKSLADWGRRSLEPKTEDTAEADNNNSTPKSESLLSQALEKHSNVSSMYDRHLLRDNGDGRDGDSASDTTSERPESLMDGLIKNSGAESELHRQLSAASPASMGGHLFPPGLEALYRQAGFPSAFLGLAAGAA—-GGSPGG————–PVSSMHGLASSVPQVGLQSHAGNPN—————————————–LAGKLDMMRVRATDPRPCPKCGKIYRSAHTLRTHMEDKHTICPGYRCVLCGTVAKSRNSLHSHMSRQHRGISTKDLPVLPMPSPFDPALASRLLAKAGVKVTPNELAARASPTAPRRSDLPKLDTNLLHM-HHHQFPLPPSLPT-SMSGHMGRGSHDGNGSDVEDLRVSSAPSPFGSNGGPGGIYSQAHQMRIAQGMLSPKDFA–ALASAGGAQGAAGMGSALLDTYLSMI-AAAGGDSNPMAAALNFQ-NPASRAAAFAAAAAAASGNQAHNGDGKDNDQRSGVSEDRDDMTGELGSDADNDDLSDNDD 661 D++ P PKRHR NG E…
Interferon-gamma is quintessential for NOS2 and COX2 expression in ER- breast tumors that lead to poor outcome
Cell culture The MDA-MB231 (MB231) human breast cancer cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA) and grown in RPM1-1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen, Waltham, MA) at 37 °C in a humidified atmosphere of 5% CO2 in the air. Cells were…
Promising Scholars Recognized with McCrone Awards | Humboldt NOW
Cal Poly Humboldt professors Oscar Vargas, Biological Sciences; Paul Michael Leonardo Atienza, Critical Race, Gender & Sexuality Studies (CRGS); and Rouhollah Aghasaleh, School of Education, are recipients of the 2023 McCrone Promising Faculty Scholars Award. Selected for exhibiting potential in a specific field, each faculty member will receive $1,500 to…
How much can I rely on DNA segments less than 8CM
Part 2 A brief summary of the data is at this Google Sheet. I’ve been (casually, not earnestly) thinking about trying to locate a child and both parents who have done a 30X WGS or better, and at least a couple of their cousins (preferably 2nd through 4th) who also have…
Aerial transport of bacteria by dust plumes in the Eastern Mediterranean revealed by complementary rRNA/rRNA-gene sequencing
Katra, I. et al. Richness and diversity in dust stormborne biomes at the Southeast Mediterranean. Sci. Rep. 4, 5265 (2014). Article CAS Google Scholar Kellogg, C. A. & Griffin, D. W. Aerobiology and the global transport of desert dust. Trends Ecol. Evolution 21, 638–644 (2006). Article Google Scholar Mazar, Y.,…
R: PC gamma
PCgamma {GSAgm} R Documentation PC gamma Description For GSA of SNP data, the following two-step procedure is implemented (see Biernacka et al[1] for more details on the method). Step 1: Principal components analysis for SNPs within a gene is completed with the components needed to explain 80 percent of the…
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…
17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze
Background: Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA-expression at birth on development of wheeze. Methods: Children were classified as…
I can’t get a dossage file using PLINK
Hi, I have been trying to get a dosage file from vcf, map and fam files. For that, I have written this bash script : plink –fam plink.fam –map plink.map –dosage one.vcf –write-dosage However, I got this error: –dosage: Reading from one.vcf. Error: Line 1 of one.vcf has fewer tokens…
Phasing with SHAPEIT
Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…
Single cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma
Footnotes Grant support This work is jointly supported by National Natural Science Foundation of China (82173035, 81802813,82030079, 81972656, 81988101, and 81902401), the National Science and Technology Major Project of China (2018ZX10723204), the Michigan Medicine and Peking University Health Science Center Joint Institute for Translational and Clinical Research (BMU2020JI005), Natural Science…
working with .gmt files
working with .gmt files 3 Hi! I have downloaded a pathway data set in .gmt format form the GSEA website. I’m wondering how can I properly read this data set in R. Could anyone help me? Thank you! myposts • 9.5k views • link updated 2 hours ago by…
