Category: indel

Laniakea@ReCaS: exploring the potential of customisable Galaxy on-demand instances as a cloud-based service | BMC Bioinformatics

Since the opening of the open-ended Call in February 2020 [30], Laniakea@ReCaS has accepted ten project proposals for a total of 18 Galaxy instances operating on the ReCaS infrastructure that altogether launched almost 30 k jobs, as of March 2021 (Fig. 3). Fig. 3 Cumulative number of jobs launched by all the…

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Color hiring Bioinformatics Scientist in Chicago, Illinois, United States

Named by Rock Health as the Best Digital Health Company to Work For , Color is a leading healthcare technology company. Color is building and delivering technology-enabled healthcare to millions of people. Through partnerships with public and private partners including governments, employers and health systems, Color’s infrastructure and software enables…

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Color hiring Bioinformatics Engineer in Atlanta, Georgia, United States

Named by Rock Health as the Best Digital Health Company to Work For , Color is a leading healthcare technology company. Color is building and delivering technology-enabled healthcare to millions of people. Through partnerships with public and private partners including governments, employers and health systems, Color’s infrastructure and software enables…

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Detection of heteroplasmy and nuclear mitochondrial pseudogenes in the Japanese spiny lobster Panulirus japonicus

Direct nucleotide sequencing Readable electropherograms were obtained from both direction in COI fragments of all three individuals of the Japanese spiny lobster. COI sequences determined by direct nucleotide sequencing ranged from 807 to 864 bp and have been deposited in International Nucleotide Sequence Database Collection (INSDC) under accession numbers of LC571524‒LC571526….

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Shaping modern human skull through epigenetic, transcriptional and post-transcriptional regulation of the RUNX2 master bone gene

Study of RUNX2 locus in modern and ancient humans The sequences of the RUNX2 locus (Chr6:45,318,000–45,670,000 hg38, for a total of 352.000 bases) have been aligned in AMH and ancient species’ (Neandertal and Denisovan) genomes to map the changes occurred during recent evolution. We have identified 459 and 470 changes…

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Ensembl variant consequences and classification info in table format

Ensembl variant consequences and classification info in table format 1 using xsltproc with the following stylesheet: <?xml version=”1.0″ encoding=”UTF-8″?> <xsl:stylesheet xmlns:xsl=”http://www.w3.org/1999/XSL/Transform” version=”1.0″> <xsl:output method=”text”/> <xsl:template match=”https://www.biostars.org/”> <xsl:apply-templates select=”//table[@id=’variation_classes’]/tr”/> </xsl:template> <xsl:template match=”tr”> <xsl:for-each select=”th|td”> <xsl:value-of select=”normalize-space(.)”/> <xsl:text> </xsl:text> </xsl:for-each> <xsl:text> </xsl:text> </xsl:template> </xsl:stylesheet> usage: $ wget -q -O – “https://www.ensembl.org/info/genome/variation/prediction/classification.html#classes” |…

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How to merge different VCF files

How to merge different VCF files 0 Hi everyone, I have 2 different VCF files (v4.3) : one containing SNP and Indels and the other one containing CNVs. The latter has only the mandatory fields (CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO) while the former has also the field…

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BAMboozle removes genetic variation from human sequence data for open data sharing

Strategy for stripping human sequence data of genetic information To lower the barriers in sharing sequence data, we propose, like others recently17, to remove information on genetic variation that could be used to infer the identity from aligned reads and compromises the privacy of the donor (Fig. 1a). Genetic variation, including…

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Further and More Detailed Study of Domestic Cat Genome | McDonnell Boehnen Hulbert & Berghoff LLP

The advent of technology making feasible elucidation of whole genomic sequencing over the past 30 years has led to reports of many if not most important or interesting animal genomes (including the most celebrated results of the Human Genome Project) (see, e.g., “Nautilus pompilius Genome Determined“; “Giraffe Genome Reveals Relevant…

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Samtools mpileup – I’m getting different number of base calls compared to number of quality scores

Edit: Summary: In the mpileup file, I have different number of quality scores than base calls. For example, I might have 342 reads covering a position, but there will be 340 base calls. This makes parsing the mpileup file difficult Edit: I should note that the mpileup I’m using was…

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Removing indels +/- a buffer area? How? : bioinformatics

Hey everyone. Hopefully an easy question but my Googling and looking for papers hasn’t really come up with much. I am using a software (IBDMix) to analyze some Neanderthal DNA vs. Modern humans using the new HG38 1000 Genomes data from earlier this year. The method in the IBDMix paper…

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gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz)

gatk legacy bundles (where to get Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz) 0 I need the known indels vcf to run gatk BaseRecalibrator. So I need hg19 (not the b37) version of the known indels: Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz However this file is no longer available at: ftp://gsapubftp-anonymous@ftp.broadinstitute.org/bundle/hg19/Mills_and_1000G_gold_standard.indels.hg19.sites.vcf.gz the broad institute documentation says the ftp site was disabled…

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ProPIP: a tool for progressive multiple sequence alignment with Poisson Indel Process | BMC Bioinformatics

Here we present the ProPIP software, which implements our originally published progressive MSA inference method based on PIP [7], and also introduces new features, such as stochastic backtracking and parallelisation (as described below). According to the PIP model, insertions are Poissonian events on a phylogeny that add single characters to…

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Bioinformatics Scientist II – 64019 Jobs in Philadelphia, PA – Children’s Hospital of Philadelphia

Location: LOC_ROBERTS-Roberts Ctr Pediatric Research Req ID: 113752 Shift: Days Employment Status: Regular – Full Time Job Summary The Bioinformatics Unit (BIXU) within the Center for Data Driven Discovery (D3b) at The Children’s Hospital of Philadelphia (CHOP) is seeking a level II Bioinformatics Scientist to join our over 30 professional…

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Bioinformatics Scientist (Genome) in Bethesda, MD

Position Objective: Provide services as a Bioinformatics Scientist in support of the overall functions of the National Human Genome Research Institute (NHGRI) within the National Institutes of Health (NIH). Duties and Responsibilities: + Generate and optimize programs and scripts for the analysis of data; create programs and algorithms and develop…

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Factors influencing multidrug-resistant tuberculosis | IDR

Introduction Pediatric tuberculosis (TB) is a significant global health threat and is one of the top ten causes of death in children.1 Globally, in 2019, an estimated 10.0 million people fell ill with TB, with children (aged under 15 years old) accounting for 12%, causing 1.4 million deaths.2 With the…

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when should I use VQSR or hard filtering?

GATK site filtering: when should I use VQSR or hard filtering? 0 I’m always unsure whether to use VQSR or hard filtering when I do site filtering after joint-calling using GATK. One reasonable criterion I can think of is to inspect the structure of the VQSR model (that 2D heatmap…

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NM_182961.4(SYNE1):c.21155_21156delinsTT (p.Gly7052Val) AND not provided – ClinVar

NM_182961.4(SYNE1):c.21155_21156delinsTT (p.Gly7052Val) AND not provided Based on: 1 submission [Details] Record status: current Accession: RCV000597527.1 Allele description [Variation Report for NM_182961.4(SYNE1):c.21155_21156delinsTT (p.Gly7052Val)] NM_182961.4(SYNE1):c.21155_21156delinsTT (p.Gly7052Val) Gene: SYNE1:spectrin repeat containing nuclear envelope protein 1 [Gene – OMIM – HGNC] Variant type: Indel Cytogenetic location: 6q25.2 Genomic location: Preferred name: NM_182961.4(SYNE1):c.21155_21156delinsTT (p.Gly7052Val) HGVS:…

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Single-cell Analysis of Genome Engineering | Learning Center

ENGINEERED CELLS & SINGLE-CELL ANALYSIS Many of today’s cutting-edge research methods and therapies rely on the engineering of cells. By precisely altering DNA, genome engineering makes it possible to probe the relationship between a gene and its function, repair dysfunctional genes, or add functionality to cells. Changing the genome often involves…

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A rapidly reversible mutation generates subclonal genetic diversity and unstable drug resistance

Different mechanisms of adaptation have different timescales. Epigenetic changes are often rapid and reversible, while most genetic changes have nearly negligible rates of reversion (1). This poses a challenge for genetic adaptation to transient conditions such as drug treatment; mutations that confer drug resistance are often deleterious in the absence…

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Rsubread FeatureCounts return 0.0% assigned

Using featureCounts in the Rsubread package I am getting 0 annotations. I started from raw sequencing data and the Refseq genome and Refseq Genomic GTF files downloaded from here: www.ncbi.nlm.nih.gov/assembly/GCF_000001635.27/ through the download assembly button on the side. I had the top option to RefSeq for both downloads and chose…

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sanger method of dna sequencing flow chart

Flowchart Describing Assembly And Annotation Procedures The . Flow Chart Summarizing The Procedure For Identifying The Dna . Sangers Method Of Gene Sequencing Online Biology Notes . Sanger Sequencing Wikipedia . Flow Chart For The Analysis Of A Metagenome From Sequencing . Dna Sequencing Article Biotechnology Khan Academy . Flowchart…

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Comparison of sequencing data processing pipelines and application to underrepresented African human populations | BMC Bioinformatics

Literature survey We reviewed the processing pipelines of 29 HTS studies, 23 of which focus on human populations and six on other mammals (listed in Table 1). Table 1 List of studies included in the literature survey We summarized the information for some processing steps in Table 2 (see Additional…

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Reference genome version between variant calling and annotation

Question: Reference genome version between variant calling and annotation 0 Dear colleagues, My project is focused on the annotation of human genetic variants (SNPs and short InDels) of WGS and WES. I am using SNPEff version 5.0. In the snpeff config file I found GCA_000001405.28_GRCh38.p13 Homo sapiens (hg38) (UCSC). In…

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Index of /examples/archive/bioinfo/samtools

Index of /examples/archive/bioinfo/samtools Samtools/BCFtools/HTSlib Introduction and Notes Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories: Samtools Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format BCFtools Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants HTSlib A C library for reading/writing high-throughput sequencing data…

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Cis-acting mutation affecting GJA5 transcription is underlying the Melanotic within-feather pigmentation pattern in chickens

Significance The molecular mechanisms underlying pigmentation patterns in animals is to a large extent an unresolved mystery in biology. For example, compared with mammals, birds show a stunning diversity in pigmentation patterns. This study advances the knowledge concerning the mechanisms creating periodic pigmentation patterns in individual feathers. We show that…

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Pindel fix to allow compilation on Debian 9.0

Pindel fix to allow compilation on Debian 9.0 0 I recently had some trouble compiling Pindel in a recent Debian release: the gcc compiler aborts after some errors related to the (in)existence of the overloaded function abs(unsigned int). Though googling the issue quickly finds an answer in the form of…

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Rainbow Genomics Launches Pan-Cancer Test to Detect Genomic Rearrangements and Genetic Disorders Associated with Cancers

Evidence-Based Genomic Testing Dual Large Genomic Rearrangement Sequencing and Whole Exome Sequencing Increases Diagnostic Yields for Hereditary Cancer Patients and Asymptomatic Individuals SAN FRANCISCO, CALIFORNIA, UNITED STATES, October 3, 2021 /EINPresswire.com/ — Hong Kong and U.S. based Rainbow Genomics announced today the introduction of the Rainbow Pan-Cancer(TM) Test, to determine…

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Type of analyses Which can be performed on Whole Genome Data

Type of analyses Which can be performed on Whole Genome Data 1 Hey everyone, This might be a nieve question, kindly spare me. I want to know about type of analyses which can be performed on whole genome sequence data. For example, say I have whole genome data of like…

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Crossing design shapes patterns of genetic variation in synthetic recombinant populations of Saccharomyces cerevisiae

Population creation All yeast strains used in this study originated from heterothallic, haploid, barcoded derivatives of the SGRP yeast strain collection30. A subset of 12 of these haploid strains, originally isolated from distinct geographic locations worldwide, were used to create the synthetic populations we describe here (See Supplementary Fig. S1…

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Chromosome-level genome assemblies of five Prunus species and genome-wide association studies for key agronomic traits in peach

Genome assembly In this study, we de novo assembled the plum, Prunus mira, and Prunus davidiana genomes for the first time and improved the peach and apricot genomes by integrating single-molecule real-time (SMRT) long-read sequencing (PacBio), short high-quality Illumina paired-end sequencing, and Hi-C technology. First, we used SMRT reads (99−130 Gb,…

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Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)

NB – Update July 29, 2020 – this thread will no longer be watched and, for all intents and purposes, will now be archived NB – Version 2 of tutorial can be found here and should be used going forward –> Produce PCA bi-plot for 1000 Genomes Phase III –…

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whole genome sequencing method

steps Collect and isolate the DNA or genome. WGS techniques generate from bacterial samples multiple short reads that can be assembled based on overlapping regions (de novo assembly), and/or mapped to a previously published reference genomes, which then enable the comparison between bacterial strains that genetically diverge at a single…

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Split a VCF file into individual sample files

Split a VCF file into individual sample files 4 I have the thousand genomes VCF file such as the following ALL.chrX.integrated_phase1_v3.20101123.snps_indels_svs.genotypes.vcf.gz and this contains all the samples data in many, many columns. I want to split this file into separate VCF files, one for each sample. I tried the following…

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Is it possible to construct a full genome from whole sequence VCF files containing snp, indel, sv, cnv data?

Is it possible to construct a full genome from whole sequence VCF files containing snp, indel, sv, cnv data? 1 I’m wondering how one might go about reconstituting the whole genome by combining VCF data with the reference data GRCh37? Are there any tools for this? Thank you in advance…

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Plasmodium falciparum is evolving to escape malaria rapid diagnostic tests in Ethiopia

Study design and data collection We performed a cross-sectional, multisite study in 11 districts along Ethiopia’s borders with Eritrea, Sudan and South Sudan, located within three of its nine administrative regions. On average, ten health facilities were selected from each district, including four districts of Amhara Region (northwest Ethiopia), six…

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Cutadapt de-multiplexing does not recognize some barcodes

Hey all, So I currently dealing with deep-sequencing data of 16S amplicons from multiple variable regions on the 16S gene. I used different sets of primers to amplify different regions and then sequenced them all together, I am trying to de-multiplex based on those primers using cutadapt and the following…

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In vitro genome editing rescues parkinsonism phenotypes in induced pluripotent stem cells-derived dopaminergic neurons carrying LRRK2 p.G2019S mutation

This article was originally published here Stem Cell Res Ther. 2021 Sep 22;12(1):508. doi: 10.1186/s13287-021-02585-2. ABSTRACT BACKGROUND: The c.G6055A (p.G2019S) mutation in leucine-rich repeat kinase 2 (LRRK2) is the most prevalent genetic cause of Parkinson’s disease (PD). CRISPR/Cas9-mediated genome editing by homology-directed repair (HDR) has been applied to correct the…

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Molecular differences in mitochondrial DNA (mtDNA) genomes of dogs with malignant mammary tumours

doi: 10.1111/vco.12772. Online ahead of print. Affiliations Expand Affiliations 1 Institute of Biological Bases of Animal Production, University of Life Sciences in Lublin, Lublin, Poland. 2 Department of Genomics and Biodiversity, Institute of Genetics and Animal Biotechnology, Polish Academy of Sciences, Poland. 3 DNA Sequencing and Synthesis Facility, Institute of…

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Recommendation for computational tools to detect gene editing induced INDELs from amplicon NGS data

Recommendation for computational tools to detect gene editing induced INDELs from amplicon NGS data 0 I am looking for a software program to detect INDELs in zinc-finger nucleases (ZFNs)-edited genes using amplicon sequencing data. The purpose is to evaluate the gene-editing efficiency. After hours of literature search, I found most…

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Does the SOAP (BGI) website mirror exist

Does the SOAP (BGI) website mirror exist 0 Hi! It seems that SOAP (BGI) website enter link description here is not currently available. But i need a soap2.21 and soapInDel from their SOAP suite. Perhaps it shoulbe within SOAP2. Where can i find the SOAP (BGI) website mirror or at…

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GenomSys – Bioinformatics and genomics

By Luca Trotta on September 29, 2021 As described in last months’ articles, genomic methods are increasingly and effectively used to support diagnostic, preventive, and therapeutic strategies and enhance the development of personalized medicinal approaches. Please find our previous articles here: Genomic Corner  Evolution of genomics Genomics is the study…

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Flavivirus-GLUE by giffordlabcvr

Overview The flaviviruses (family Flaviviridae) are a group of enveloped, positive-strand RNA viruses, many of which pose serious risks to human health on a global scale. Arthropod-borne flaviviruses such as Zika virus (ZIKV), Dengue virus (DENV), and yellow fever virus (YFV) are the causative agents of large-scale outbreaks that result…

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Strange speed up in GATK LeftAlignIndels

Strange speed up in GATK LeftAlignIndels 1 Hi! I noticed a strange thing, I have been running a DNA-seq pipeline like this: reads -> bwa-mem2 -> picard SortSam -> picard MergeSamFiles -> picard MarkDuplicates -> gatk LeftAlignIndels … gatk LeftAlignIndels has always taken around 4 hours to complete with the…

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Data Demonstrates Lucence Liquid Biopsy Test Can Track Treatment-Based ctDNA Changes

NEW YORK – At the European Society for Medical Oncology Congress this week, precision oncology assay developer Lucence presented data that demonstrated its amplicon-based LiquidHallmark assay could be used to personalize care for people with advanced urothelial carcinoma. LiquidHallmark is a laboratory-developed test based on the company’s AmpliMark next-generation sequencing platform…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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Ttc30a affects tubulin modifications in a model for ciliary chondrodysplasia with polycystic kidney disease

Significance Cilia are tubulin-based cellular appendages, and their dysfunction has been linked to a variety of genetic diseases. Ciliary chondrodysplasia is one such condition that can co-occur with cystic kidney disease and other organ manifestations. We modeled skeletal ciliopathies by mutating two established disease genes in Xenopus tropicalis frogs. Bioinformatic…

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iCOMIC: a graphical interface-driven bioinformatics pipeline for analyzing cancer omics data

Abstract Despite the tremendous increase in omics data generated by modern sequencing technologies, their analysis can be tricky and often requires substantial expertise in bioinformatics. To address this concern, we have developed a user-friendly pipeline to analyze (cancer) genomic data that takes in raw sequencing data (FASTQ format) as input…

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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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PolyAllele Detail

Polymorphism: FLAG_344G02 Name    FLAG_344G02 Date last modified    2006-09-11 Aliases    344G02 Tair Accession    Polymorphism:1009991284 Type    insertion    Insertion Type    T-DNA Chromosome   unknown Mutagen    T-DNA insertion Mutation Site    gene Associated Polymorphisms Insertion   Species Variant (attribution)   Length   Polymorphic Sequence   Polymorphism…

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gnomAD v3 link not working for download

gnomAD v3 link not working for download 1 your URL is wrong. $ wget -q -O – “https://storage.googleapis.com/gcp-public-data–gnomad/release/3.1.1/vcf/genomes/gnomad.genomes.v3.1.1.sites.chr1.vcf.bgz” | gunzip -c | head ##fileformat=VCFv4.2 ##hailversion=0.2.64-1ef70187dc78 ##FILTER=<ID=AC0,Description=”Allele count is zero after filtering out low-confidence genotypes (GQ < 20; DP < 10; and AB < 0.2 for het calls)”> ##FILTER=<ID=AS_VQSR,Description=”Failed VQSR filtering…

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Beagle 5.2 Imputation Issue, understanding output

Hey everyone, I’m having some trouble with the imputation step in my GBS pipeline. I’m following the FastGBS pipeline basically as written up until this point. Before running Beagle, i’ve performed a filtering step using vcftools (though I get the same error whether or not I do this; I just…

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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…

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SNP exon region UCSC

SNP exon region UCSC 2 how i can get SNP in only exons regions genome with UCSC? UCSC get the all SNP of gene region, and there is no filter option to get only exon region. tx ucsc SNP exon • 245 views • link updated 2 hours ago by…

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High tumor mutation burden and DNA repair gene mutations

Introduction Anaplastic lymphoma kinase (ALK)‑fusion genes represent a small but important part of oncogenic driver mutations in NSCLC, accounting for approximately 3%‑7% of all cases worldwide.1,2 Small molecule tyrosine kinase inhibitors (TKIs) are the standard therapy for ALK-rearranged NSCLC. Crizotinib, a first-generation TKI, is the most widely used targeted drug…

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Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory

The mammalian genome is characterized by widespread methylation of cytosine residues. After fertilization, however, both maternal and paternal genomes undergo extensive demethylation, reaching a low point in the blastocyst (1⇓⇓–4). The embryo genome is then remethylated by the activity of de novo DNA methylation enzymes (5). Mouse embryonic stem (ES)…

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Produce PCA bi-plot for 1000 Genomes Phase III

Note1 – Previous version: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old) Note2 – this data is for hg19 / GRCh37 Note3 – GRCh38 data is available HERE The tutorial has been updated based on the 1000 Genomes Phase III imputed genotypes. The original tutorial was…

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Filtering long indels from VCF

Filtering long indels from VCF 1 Hi, to create a multi-sample VCF in a large cohort of WES samples of very different quality I have to select only high-quality variants genotyped in as many samples as possible. I figured out that long indels have low quality only substitutions do not…

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BBMerge / Tadpole error correction

I’ve been using BBMerge recently to address a very specific problem: I am sequencing pooled short DNA molecules (< 400bps) using paired end reads (average length ~ 230 bps post trimming) Each molecule can be assumed to be different (i.e. contains sequence differences – substitutions & indels – with respect…

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ABRF Study Benchmarks NGS Platforms on Human, Microbial Samples, Provides Peek at Genapsys Data

NEW YORK – The results of a major, core facilities-driven benchmarking study for next-generation sequencing platforms are in, and just about every major player in the field can claim a victory of some sort. The data support longstanding advantages touted by market leader Illumina, while also providing a sneak peak…

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Strata Oncology Trial Data Support Robustness of NGS Assay for Challenging Samples

NEW YORK – Research from Strata Oncology on a large cohort of cancer patients has shown that the firm’s amplification-based sequencing assay can handle samples that don’t meet the usual requirements for comprehensive genomic profiling (CGP). The company also believes that assays like StrataNGS that only need little tumor tissue…

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Cancer Mutation Detection Depends on Choices at Each Step of Sequencing, Analysis Pipeline

NEW YORK — An international team of researchers has examined how variations in sequencing approaches can influence the ability to accurately detect cancer mutations, providing guidance for the wider community. The team additionally developed a set of reference samples for benchmarking efforts. Next-generation sequencing approaches are increasingly being adopted to…

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PROVEAN input script

PROVEAN input script 1 Hi everyone, I would like to write a python script to extract amino acid substitutions and indels from several protein alignments, and use it as an input for variant effect prediction with PROVEAN. So far I have modified an initial script (C: How to extract polymorphic…

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Using UnifiedGenotyper on single chromosome without coordinates

Using UnifiedGenotyper on single chromosome without coordinates 0 I have a large number of bam files, containing subsets that were aligned against (slightly) different reference genomes that were created to account for differences in indel distributions etc across different populations. I am specifically interested in genetic variation in the X…

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Oncogene Concatenated Enriched Amplicon Nanopore Sequencing for rapid, accurate, and affordable somatic mutation detection | Genome Biology

Stochastic Amplicon Ligation. DNA samples for oncology sequencing are typically extracted from FFPE tissues and can have average lengths of less than 500 nt due to accumulated chemical damage [18]. We developed the Stochastic Amplicon Ligation (SAL) method to enzymatically concatenate many short DNA molecules together to utilize the long-read…

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How To Uncompress The 1000 Genome Vcf.Gz File

How To Uncompress The 1000 Genome Vcf.Gz File 2 Hello, Can somebody tell me how to uncompress 1000 Genome vcf.gz files? I am performing an RNA-editing analysis and would like to substract annotated SNPs/INDELs. I have already done so using dbSNP data with bedtools instersect, but am still stuck with…

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VCFtools doesn’t keep any variants using GATK output

Hi guys! I’m having trouble using vcftools to filter snp through GATK output. For infomation, i used the command HaplotypeCallerto make SNP-calling of 12 samples ; i used the CombineGVCFs to join the 12 VCFS and make the joint call after merging the vcf files; i used the VarianFiltration for…

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Job vacancy in Global Worldwide: Bioinformatics Scientist III – D3b at Children`s Hospital of Philadelphia

Job details Job type full-time Full job description Location: loc_roberts-roberts ctr pediatric research req id: 134035 shift: days employment status: regular – full time job summary the bioinformatics unit (bixu) within the center for data driven discovery (d3b) at the children’s hospital of philadelphia (chop) is seeking a level iii…

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Rsubread align maximum nthreads

Hi Experts, I am using Rsubread align using following comand- align (index=”my_index”, readfile1 = “SRR123456_1.fastq” ,readfile2= “SRR123456_2.fastq”, type=”rna”,input_format = “FASTQ”, minFragLength=35,maxFragLength=151,useAnnotation=”TRUE”, nthreads=64, annot.ext = “my_annotation.gtf.gz”, isGTF = “TRUE”, sortReadsByCoordinates = “TRUE”, output_format = “BAM”) here i have asigned 64 threads but in console, i see only 40 threads, I dont…

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Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data?

Is it possible to detect of SNVs and InDels in low coverage WGS (5-10X) data? 2 Hello, the Biostar community, What I know about low coverage WGS (or shallow WGS) data is that it is an economic technique for genomic copy number detection in the realms of tumor diagnosis or…

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Truncating alignments in a SAM/BAM file

Truncating alignments in a SAM/BAM file 0 Hi everyone, I am interested in narrowing or truncating the alignment of reads in SAM or BAM formatted files by X NTs from each end. My reason is that the detection of indels is a bit muddied by a percentage of reads reaching…

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CRISPR-Based Therapeutics Blaze an In Vivo Path to the Clinic

Therapeutic applications of genome editing were envisioned at least as early as the mid-1990s, when the first sequence-specific genome editing technologies emerged. Initially, such applications were considered distant prospects, but by 2012, they suddenly seemed near to hand. It was at that time that CRISPR technologies emerged. CRISPR, which stands…

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Industrializing CRISPR

Sponsored content brought to you by Kevin Holden, PhD Kevin Holden, PhD, Head of Science at Synthego, discusses the importance of industrializing CRISPR as the technology matures and makes inroads in the clinic. GEN: What’s new and interesting to you in the world of CRISPR? HOLDEN: Some of the most…

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New Techniques and Complex Models

CRISPR systems that rely on inactivated Cas enzymes—that is, dead Cas (dCas) enzymes—never looked more alive. They harness the targeting power associated with CRISPR—but not the double-strand cuts. As such, they give researchers new ways to interrogate and manipulate gene function. Possibilities include CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa)…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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snp analysis

snp analysis 1 Hello everyone, I got these images from a senior student. I don’t know how to interpret this graph. I know that its referring to minor allele frequency distribution. But why there is sharp peak near one and then there is decline. For this graph, I know its…

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Multiform antimicrobial resistance from a metabolic mutation

Abstract A critical challenge for microbiology and medicine is how to cure infections by bacteria that survive antibiotic treatment by persistence or tolerance. Seeking mechanisms behind such high survival, we developed a forward-genetic method for efficient isolation of high-survival mutants in any culturable bacterial species. We found that perturbation of…

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problems with snippy on galaxy

problems with snippy on galaxy 0 Hello I have a few questions regarding snippy. I need to analyze around 20 genomes and compare them to reference genome. I used unicycler to assemble my reference genome from illumina short reads and Pacbio long reads and then I used snippy to find…

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Validation of gene editing efficiency with CRISPR-Cas9 system directly in rat zygotes using electroporation mediated delivery and embryo culture

doi: 10.1016/j.mex.2021.101419. eCollection 2021. Affiliations Expand Affiliations 1 Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA. 2 Cystic Fibrosis Research Center, Division of Pulmonary, Allergy, and Critical Care Medicine, University of Alabama at Birmingham, Birmingham, AL, USA. Free PMC article Item in Clipboard Anil K Challa et al….

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Genomics Could Again Be Prime Time Idea

As experienced investors know, it takes some patience to engage with genomics stocks. That’s just the lay of the land with one of the more volatile, yet promising, growth-rich corners of the healthcare sector. Exercising that patience can be made easier when accounting for the catalyst-rich story that is the…

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the Genomic Rearrangement IDentification Software Suite

Tool:GRIDSS: the Genomic Rearrangement IDentification Software Suite 0 GRIDSS is typically used for detecting structural variation breakpoints from short read sequencing data but is a modular software suite containing a number of tools useful for the detection of genomic rearrangements including: A structural variant caller. The GRIDSS caller uses break-end…

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Strong within-host selection in a maternally inherited obligate symbiont: Buchnera and aphids

Significance Many animals depend on maternally transmitted symbiotic bacteria that provide nutrients or other benefits. The evolution of these symbionts is complicated: natural selection can act on hosts, favoring symbionts that increase host reproduction, or on symbionts, favoring symbionts that spread within hosts. Furthermore, transmission bottlenecks can facilitate the spread…

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Psyt 502 error

Psyt 502 error 25-08-2021 PSYT Issues in Drug Dependence 3 Credits PSYT Brain Evolution & Psychiatry 3 Credits PSYT Advanced Studies in Addiction 3 Credits. Syntax Error. Usage: dbname:identifier. KEGG, ENZYME: , Help. Entry. EC Enzyme….

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Blocking Melanin to Boost Commercial Demand for Tilapia

Source: The CRISPR Journal Scientists at Israel’s Agricultural Research Organization (ARO), Volcani Center in Rishon Lezion, have used CRISPR-Cas9 genome editing tools to create a new strain of tilapia that does not develop suspicious blotches on their skin and instead acquires appealing, uniform, red skins that drive up their commercial…

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CRISPR: Guide to gRNA design

Introduction to CRISPR in SnapGene Genome editing technology has been evolving for many years. The Holy Grail of genome engineering has always been to introduce a specific genetic change that affects only the genomic target and leaves no undesired changes in the DNA. The discovery and application of the bacterial…

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Dissecting Cancer with Single-cell DNA Sequencing & Multi-omics | Learning Center

CANCER & SINGLE-CELL ANALYSIS The heterogeneity and dynamism of cancer present formidable challenges to understanding and treating the disease. As discussed in the last section, tumor evolution often leads to considerable genetic variation across clones. But the complexity of tumors does not stop at the level of DNA. Intratumoral phenotypic…

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How to merge multiple patient’s vcf files (indel and snv) with different IDs?

How to merge multiple patient’s vcf files (indel and snv) with different IDs? 0 Hi all, I have some VCF files for my patients, each patient has 2 files( indel.vcf , snv.vcf) and I want to merge these file by the script bellow: java -jar gatk-package-4.2.0.0-local.jar MergeVcfs -I /PATH_TO_patient1_ID_indel.vcf -I…

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samtools returns error – cigar and query sequence are of different length even though cigar and query sequence are the same length

samtools returns error – cigar and query sequence are of different length even though cigar and query sequence are the same length 1 I have written a program in python that processes and outputs mapped results as either a bam or sam file. It works fine until I have indels…

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Need suggestions about pathogenicity prediction of gdc level 3 SNV file

Hi, I am trying to figure out which tool is most accurate in terms of pathogenicity prediction of TCGA SNVs level 3 data. TCGA offers SIFT, PolyPhen, and IMPACT scores for different kinds of mutations. SIFT, and PolyPhen cover mainly “Missense Mutation”, while IMPACT categorizes every kind of mutation into…

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VcfSampleCompare – empty output with warnings

Hello to all, I have 10 vcf files – 5 female fish and 5 male fish, I have merged all 10 fish to one vcf file.(all_fish.vcf) I performed the VcfSampleCompare analysis on ‘all_fish.vcf’ , following this:github.com/hepcat72/vcfSampleCompare The example command : vcfSampleCompare.pl –sample-group ‘wt1 wt2 wt3’ –sample-group ‘mut1 mut2 mut3’ input.vcf…

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Filter on Allele Balance using BCFTools

Filter on Allele Balance using BCFTools 0 Hi All, I need to filter my variants based on the following criteria. 1) Include SNP sites with at least one heterozygous with allele balance(AB) > 0.15 or at least one homozygous variant 2) Include INDEL sites with at least one heterozygous with…

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KING struggle: Relatedness

I struggle to infer relationships in a dataset of 20K exomes from tens of kits. At first I found a well-covered union of regions – check. Second, I performed everything to merge 20K VCFs into one. Removed indels and multi-allelic variants. Check. Still, when I run KING with “kinship” option,…

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So many variants detected.

So many variants detected. 0 Dear All, I have done variant calling in Germline data that has single sample of each individual and two genes. I did following steps, but after checking results I found too many variants. After Haplotypecaller (the step 6) I found 140900 known variants, and the…

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How to identify mutations from FASTA sequences?

How to identify mutations from FASTA sequences? 0 I have two full genome sequences (in Fasta format) plus annotation file (in gff format) from same organism. One sequence is the reference genome and another is my test sequence. Would you please suggest me some pipeline or tools ( preferably, R…

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