Tag: LD

Adding ions ‘gmx grompp’ creates error “Atomtype ca not found” for ligand generated with GAFF – User discussions

GROMACS version: 2018GROMACS modification: No Hello, I am trying to run 200ns on protein-ligand complex and then calculate MMPBSA for the last 100 ns generated frames. I had some problems with ligand parameterization with cgenff, hence I used gaff…I have: GAFF to generate parameters for the ligand acpype to convert…

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Gst-nvivafilter – Jetson AGX Xavier

Platforms: Jetson AGX Xavier Jetpack 4.5 Cuda 10.2 IMX274 camera Hi fellow developers, I am having difficulties at making custom CUDA implementation. I have succesfully run the below pipeline. gst-launch-1.0 nvarguscamerasrc ! ‘video/x-raw(memory:NVMM), width=(int)3840, height=(int)2160, format=(string)NV12, framerate=(fraction)60/1’ ! nvivafilter cuda-process=true customer-lib-name=”libnvsample_cudaprocess.so” ! ‘video/x-raw(memory:NVMM), format=(string)NV12’ ! nvvidconv ! nvegltransform ! nveglglessink…

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Time-course RNASeq of Camponotus floridanus forager and nurse ant brains indicate links between plasticity in the biological clock and behavioral division of labor | BMC Genomics

1. Sharma VK. Adaptive significance of circadian clocks. Chronobiol Int. 2003;20(6):901–19. PubMed  Google Scholar  2. Paranjpe DA, Sharma VK. Evolution of temporal order in living organisms. J Circadian Rhythms. 2005;3(1):7. PubMed  PubMed Central  Google Scholar  3. Yerushalmi S, Green RM. Evidence for the adaptive significance of circadian rhythms. Ecol Lett….

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Long non-coding RNA MSTRG.81401 short hairpin RNA relieves diabetic neuropathic pain and behaviors of depression by inhibiting P2X4 receptor expression in type 2 diabetic rats

1. Nicodemus JM, Enriquez C, Marquez A, Anaya CJ, Jolivalt CG (2017) Murine model and mechanisms of treatment-induced painful diabetic neuropathy. Neuroscience 354:136–145. doi.org/10.1016/j.neuroscience.2017.04.036 CAS  Article  PubMed  Google Scholar  2. Morimoto SS, Kanellopoulos D, Manning KJ, Alexopoulos GS (2015) Diagnosis and treatment of depression and cognitive impairment in late life….

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The Genetic Architecture of Sleep Health Scores in the UK

Introduction Sleep is a complex neurological and physiological state. It is defined as a natural and reversible state of reduced responsiveness to external stimuli and relative inactivity, accompanied by a loss of consciousness.1 Sleep disorders can be classified as seven major categories: insomnia disorders, sleep-related breathing disorders, central disorders of…

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docx files fail to open in RStudio on Debian (at least 11) – Java rstudio

System details RStudio Edition : Dektop RStudio Version : 1.4.1717 and 2021.09.0+350 OS Version : Debian 11 R Version : 4.0.4 Steps to reproduce the problem Knit an R Markdown file to Word format. The file should be created. However, it’s not automatically opened. Click on the file in the…

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main-armv7-default][science/cp2k-data] Failed for cp2k-data-7.1.0 in stage

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: beefy12.nyi.freebsd.org/data/main-armv7-default/p772274a15b8b_s0630a06b2a/logs/cp2k-data-7.1.0.log Build URL: beefy12.nyi.freebsd.org/build.html?mastername=main-armv7-default&build=p772274a15b8b_s0630a06b2a Log: =>> Building science/cp2k-data build started at Sun Dec 19…

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Very important pharmacogene variants in the Blang population

Introduction The use of drugs should be different among diverse ethnic groups because of differences in ethnicity, age, sex, environmental factors and genetic factors. If these differences are ignored, then drug sensitivity, metabolic rate, and adverse reactions are affected, which influences the curative effect of drugs and aggravates the illness…

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How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice

How can I make sure certain SNPs are not removed during the clumping stage of PRS calculation using PRSice 1 This is a two part question. First, when implementing PRSice, is there a way to make sure certain SNPs are retained for the PRS calculation? I basically want to avoid…

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[pymc-devs/pymc] pymc3 does not work properly with lower versions of Glibc

Description of your problem I am trying to install pymc3 on a centos6 server. The various environment software versions on the server are relatively low. I used miniconda3 to create an environment to install pymc3, and I can install it successfully, but it reports an error when importing pymc3. Please…

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Reference panel data to be used for GCTA-COJO

Reference panel data to be used for GCTA-COJO 0 I performed a genome-wide meta-analysis based on summary statistics from the four cohorts to identify significant loci. Next, I would like to perform a conditional analysis using GCTA-COJO to search for SNPs independent of significant lead SNPs. I know that GCTA…

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FTBFS on riscv64, linked with -lpthread instead of -pthread

Package: fastp Version: 0.23.2+dfsg-1 Severity: normal Tags: ftbfs upstream patch User: debian-ri…@lists.debian.org Usertags: riscv64 Dear maintainer, fastp currently fails to build from source on riscv64: | g++ ./obj/adaptertrimmer.o ./obj/basecorrector.o ./obj/duplicate.o ./obj/evaluator.o ./obj/fastareader.o ./obj/fastqreader.o ./obj/filter.o ./obj/filterresult.o ./obj/htmlreporter.o ./obj/jsonreporter.o ./obj/main.o ./obj/nucleotidetree.o ./obj/options.o ./obj/overlapanalysis.o ./obj/peprocessor.o ./obj/polyx.o ./obj/processor.o ./obj/read.o ./obj/readpool.o ./obj/seprocessor.o ./obj/sequence.o ./obj/stats.o ./obj/threadconfig.o…

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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]…

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How can I calculate LD ?

How can I calculate LD ? 0 I have sequencing data in .vcf format of expanded whole exome sequencing of 2 trios (father, mother & index) one family is affected and another is not affected, I want to find out whether any linkage block is present in any one of…

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Frontiers | The cGAS-STING Pathway: A Promising Immunotherapy Target

Introduction Invaded by exogenous or endogenous pathogens, the host immune system will be activated accordingly to resist harm and maintain homeostasis, which includes innate immunity and adaptive immunity. As the first line of host immune defense, innate immunity plays a critical role in recognizing extracellular and intracellular pathogens (1, 2)….

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Ethnic Diversity of DPD activity and the DPYD Gene

Plain Language Summary Fluoropyrimidine (FP; 5-FU, capecitabine) is a common chemotherapy used to treat many different cancers, including cancer of the colon and rectum, upper digestive tract, breast and head and neck. Cancer patients who receive FP chemotherapy are at risk of developing severe side effects from their treatment. A…

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Issue with installing QIIME2 2021.11 on Windows 10 – Technical Support

Hi QIIME support team, I’m attempting to install QIIME2 on my Windows 10 machine. I installed Anaconda3, then set up conda to run in Git Bash: echo “. ${PWD}/conda.sh” >> ~/.bashrc Once I restarted Git Bash and activated Conda, I installed python-wget because installation of wget kept getting the following…

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main-arm64-default][devel/RStudio] Failed for RStudio-2021.09.1+372 in build

You are receiving this mail as a port that you maintain is failing to build on the FreeBSD package build server. Please investigate the failure and submit a PR to fix build. Maintainer: y…@freebsd.org Log URL: ampere2.nyi.freebsd.org/data/main-arm64-default/p7539e33f88ff_s169b368a62/logs/RStudio-2021.09.1+372.log Build URL: ampere2.nyi.freebsd.org/build.html?mastername=main-arm64-default&build=p7539e33f88ff_s169b368a62 Log: =>> Building devel/RStudio build started at Wed Dec 8…

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Parallel genomic responses to historical climate change and high elevation in East Asian songbirds

Extreme environments present profound physiological stress. The adaptation of closely related species to these environments is likely to invoke congruent genetic responses resulting in similar physiological and/or morphological adaptations, a process termed “parallel evolution” (1). Existing evidence shows that parallel evolution is more common at the phenotypic level than at…

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Transposition and duplication of MADS-domain transcription factor genes in annual and perennial Arabis species modulates flowering

Annual and perennial species occur in many plant families. Annual plants and some perennials are monocarpic (flowering once in their life cycle), characterized by a massive flowering and typically produce many seeds before the whole plant senesces. By contrast, most perennials live for many years, show delayed reproduction, and are…

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Issues installing Pindel from git

Issues installing Pindel from git 1 I’m currently attempting to install Pindel on my ubuntu machine (16.04 server), but have been having issues with running the ./INSTALL file. The ./INSTALL file takes the path to htslib as an argument, so I also installed htslib from git with git clone github.com/samtools/htslib

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The Current Molecular Treatment Landscape of Advanced Colorectal Cancer and Need for the COLOMATE Platform

Next-Generation Sequencing Utilizing Tumor Tissue and/or Blood The identification of actionable genomic alterations in tumors such as mCRC was once performed by Sanger DNA sequencing of tumor DNA that was extracted from fixed paraffin-embedded tumor tissue, but this has now been replaced by next-generation sequencing (NGS), which allows for larger-scale…

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Genetic basis and adaptation trajectory of soybean from its temperate origin to tropics

Resequencing of soybean accessions from low latitudes To investigate the genomic basis for the natural variation in soybean adaptation to low latitudes, we conducted whole-genome resequencing of a panel of 329 soybean accessions collected from 15 countries and covering all soybean subgroups in which 165 accessions are from in low-latitude…

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Accepted r-bioc-deseq2 1.32.0+dfsg-1 (source) into unstable

—–BEGIN PGP SIGNED MESSAGE—– Hash: SHA512 Format: 1.8 Date: Tue, 14 Sep 2021 00:18:17 +0530 Source: r-bioc-deseq2 Architecture: source Version: 1.32.0+dfsg-1 Distribution: unstable Urgency: medium Maintainer: Debian R Packages Maintainers <r-pkg-t…@alioth-lists.debian.net> Changed-By: Nilesh Patra <nil…@debian.org> Changes: r-bioc-deseq2 (1.32.0+dfsg-1) unstable; urgency=medium . [ Andreas Tille ] * Team Upload. * New…

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Identification of immunodominant Bartonella bacilliformis proteins: a combined in-silico and serology approach

Introduction Carrión’s disease is a vector-borne biphasic illness restricted to the South American Andes, with Peru as the most affected country. 1 Gomes C Pons MJ Del Valle Mendoza J Ruiz J Carrion’s disease: an eradicable illness?. The causative agent, Bartonella bacilliformis, is transmitted to humans by sandflies (Lutzomyia spp)….

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Cutoffs for Proxy Identification: D’ and R^2

Cutoffs for Proxy Identification: D’ and R^2 0 I’m using a proxy-finding script with plink that reports potential proxies with their D’ and R^2: proxy D’ R^2 9:12345698:rs12345 1.0 0.000758121 9:12345999:rs87654 1.0 0.039958 9:12346999:rs54321 1.0 0.0399958 cf. www.cog-genomics.org/plink/2.0/ld However, what cutoffs should be used? From what I’ve read, D’ is…

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How to get all genes and their annotations within a LD block?

How to get all genes and their annotations within a LD block? 0 Hi all, Thank you for your help. I identified several significant SNPs with GWAS in wheat. Next, I want to get all the genes form the haploblock where the SNPs reside. Using Emsembl, I was able to…

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Please help me understand linkage disequilibrium

I read many explanations about LD but I’m still not comfortable with the explanations. www.youtube.com/watch?v=iH8b-5BxtuY as you can see on these videos, most of them explains as if LD is about the relation between the genotype frequency of parental cell and gametes made from it. But if so, I should…

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Sequencing analysis of exons 5 and 6 in RUNX2 in non-syndromic patients with supernumerary tooth in Kelantan, Malaysia

doi: 10.1007/s00784-021-04098-x. Online ahead of print. Affiliations Expand Affiliations 1 Department of Pediatric Dentistry, Hospital Raja Permaisuri Bainun, 30450, Ipoh, Perak, Malaysia. 2 School of Dental Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia. 3 School of Dental Sciences, Universiti Sains Malaysia, 16150, Kubang Kerian, Kelantan, Malaysia. kannan@usm.my. 4…

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PLINK Haplotype blocks estimation not working

Hi, I am using PLINK to estimate haplotype blocks using Gabriel’s method. I am using the following command plink –file Chr$PBS_ARRAY_INDEX –noweb –all –blocks –ld-window-kb 500 And it seemed to be working just fine but when job finished no blocks were called at all. The log file does not mention…

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The LpoA activator is required to stimulate the peptidoglycan polymerase activity of its cognate cell wall synthase PBP1a

Significance Class A penicillin-binding proteins (aPBPs) assemble the bacterial cell wall and are the targets of penicillin and related β-lactam antibiotics. In gram-negative bacteria, the aPBPs require outer membrane lipoproteins to function. However, little is known about how these proteins promote the activity of their cognate synthases in cells. Here,…

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Problem merging data in plink

Problem merging data in plink 1 welcome everybody… In short, this is the error message that appears: Error: 4 variants with 3+ alleles present. If you believe this is due to strand inconsistency, try –flip with merge-merge.missnp. (Warning: if this seems to work, strand errors involving SNPs with A/T or…

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smartPCA: problem with .evec file

smartPCA: problem with .evec file 0 Hi all! I’m having problems with .evec file when running smartPCA. This file doesn’t consider all the individuals that I introduced in .ped file (529 individuals). Anyone knows what the problem might be? The command that I used was: ./smartpca -p Patag_sud_maf_ld.par > Patag_sud_maf_ld.out…

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Inquiry related to vcf file and formatting

Hello everyone, I am trying to run predixcan software. But its showing error as segmentation fault implying that there is something wrong with my vcf files. I am sharing the header of vcf file. ##fileformat=VCFv4.1 ##INFO=<ID=LDAF,Number=1,Type=Float,Description=”MLE Allele Frequency Accounting for LD”> ##INFO=<ID=AVGPOST,Number=1,Type=Float,Description=”Average posterior probability from MaCH/Thunder”> ##INFO=<ID=RSQ,Number=1,Type=Float,Description=”Genotype imputation quality from…

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linkage disequilibrium and haplotype analysis of GWAS .

  linkage disequilibrium and haplotype analysis of GWAS . 0   Hi all, I have GWAS data. I have my data in 22 chromosome files in plink format. I have imputed genotype with Sanger imputation server. I use plink for my analysis but because plink 1.9 no more supports –hap…

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Error in haploview data format

Error in haploview data format 0 Hi everyone , I’m trying to use haploview software to plot LD for arch chromosomes but I have tassel format data(HapMap) I converted the data to plink format via Tassel (write plink) and I have two files ,Ped file and map file , after…

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Calculate LD matrix from bgen file

formatting error: Calculate LD matrix from bgen file 1 Hello, I am new to plink and am learning as I go. I am trying to calculate an LD matrix for a list of variants while using a bgen file as my reference population. See the command below: ./plink2/plink2 –r2 bin…

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