Tag: VG

Genomic insights into Plasmodium vivax population structure and diversity in central Africa | Malaria Journal

Hamblin MT, Di Rienzo A. Detection of the signature of natural selection in humans: evidence from the Duffy blood group locus. Am J Hum Genet. 2000;66:1669–79. Article  CAS  PubMed  PubMed Central  Google Scholar  Hamblin MT, Thompson EE, Di Rienzo A. Complex signatures of natural selection at the Duffy blood group…

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Google’s VideoPoet: Revolutionizing AI Video Generation

Google’s VideoPoet: A Leap Forward in AI Video Generation Google’s latest innovation, the VideoPoet, represents a remarkable stride in artificial intelligence (AI) capabilities. This state-of-the-art video generation tool, developed using the advanced MAGVIT 2, enables users to produce high motion variable length videos with ease. Furthermore, it provides interactive editing…

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High-throughput sequencing of Diatoms using V4 region of 18S rRNA gene in Bayug Island, Iligan City, Philippines

Almarez DN, Almarez FJS, Baulete EM. 2014. Bayug Island Aquasilvi Program: An Eco-Governance Strategy for Climate Change Adaptation and Mitigation. J Govern Dev 10(2): 35-54. DOI: 10.32890/jgd. Alongi DM. 2014. Carbon cycling and storage in mangrove forests. Ann Rev Mar Sci 6: 195-219. DOI: 10.1146/annurev-marine-010213-135020. Balint M, Pfenninger M, Grossart…

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Construction of a risk stratification model integrating ctDNA to predict response and survival in neoadjuvant-treated breast cancer | BMC Medicine

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Giaquinto AN, Sung H, Miller KD, Kramer JL, Newman LA,…

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Lamz-Groups.club – Main

Registered Dec 2023 1 day old *estimated Information on this page was last updated on Dec 12, 2023 About Lamz-Groups.club The domain Lamz-Groups.club belongs to the generic Top-level domain .club. It is associated with the IPv4 addresses 104.21.76.62 and 172.67.190.86, as well as the IPv6 addresses 2606:4700:3034::ac43:be56 and 2606:4700:3037::6815:4c3e. The…

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Gripsweat – Modern Soul Boogie 45 – Terry Gengis – Ooh Sha Sha – MCA

Modern Soul Boogie 45 – Terry Gengis – Ooh Sha Sha – MCA – VG+ promo! Sold Date: December 10, 2023 Start Date: December 3, 2023 Final Price: $283.00 (USD) Bid Count: 17 Seller Feedback: 89570 Buyer Feedback: 0 Audio Clips: Media grade: VG+, light spotting on labels Listing Information…

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How to perform fungal mutagenesis?

How to DNA sequence a yeast?3 answersDNA sequencing of yeast can be done using various methods. One protocol involves preparing yeast DNA by digesting the cell wall and lysing the resulting spheroplasts with SDS. This method yields several micrograms of yeast DNA that can be cleaved by restriction enzymes and…

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Key Genes for Pyroptosis-induced Salivary Gland Inflammation

Kaiyuan Zhang,1,* Ziyue Luo,1,* Xinchao Zhu,1 Xinyi Yao,1 Dingqi Lu,2 Liying Chen,1 Tao Hong,1 Yating Ren,1 Xinchang Wang3 1Second Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China; 2First Clinical Medical College, Zhejiang Chinese Medical University, Hangzhou, Zhejiang Province, 310053, People’s Republic of China;…

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How to find node Postion and source(sample) ?

How to find node Postion and source(sample) ? 1 After constructing the graph pangenome with VG, how can I quickly transform the node information of the graph into the original linear reference coordinates (i.e., which sample a node comes from and its specific position)? vg • 155 views You can…

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systemd autopkgtest regression on arm64 and s390x on mantic

Is seems the container fails to boot. From a bad run: 9109s autopkgtest [10:39:17]: test tests-in-lxd: [———————– 9145s 2023-11-28T10:39:50Z INFO Waiting for automatic snapd restart… 9259s lxd 5.19-8635f82 from Canonical** installed 9288s Creating autopkgtest-prepare-jhI 9475s Retrieving image: metadata: 100% (323.81MB/s) Retrieving image: rootfs: 1% (3.53MB/s) <SNIP> Retrieving image: rootfs: 100%…

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Mapping quality in `vg giraffe`

Mapping quality in `vg giraffe` 0 I ran vg giraffe to get the GAF file. I have some questions about the 12th column, that is mapping quality(MAPQ). The difference of MAPQ standard between aligners makes me confused. I found MAPQ is in the range[0, 60] which similar with bwa-mem, but…

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The number of variations in the pan-genome is reduced compared to the variations in the input VCF file

The number of variations in the pan-genome is reduced compared to the variations in the input VCF file 0 Do vg filter out some variants during the construction of the pan-genome, and if so, what are the criteria for filtering? The number of variations in the pan-genome is reduced compared…

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Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject

Retrieving NM:i edit distance field in .sam files generated by vg giraffe and vg surject 0 Hello, I’m trying to compare alignment results between mapping tools, however, I’ve noticed that the .sam files I’ve made using vg surject are missing the NM:i field. Is there a way to generate a…

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Insects | Free Full-Text | Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts

1. Introduction As a representative social insect with crucial ecological, economic and scientific value, the western honey bee (Apis mellifera) is widely reared and applied in the apicultural industry in considerable countries around the world [1]. In addition, A. mellifera has been applied as a research model for development, social…

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How to obtain full alignment results?

How to obtain full alignment results? 0 Hi, When I prepare to align my short reads to the human pan-genome graph genome, the result is only a path, 1. what I want is to provide me all the sequences that have a mismatch and full alignment with this reads? And…

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Rapid Adeno-Associated Virus Genome Quantification with Amplification-Free CRISPR-Cas12a

Abstract Efficient manufacturing of recombinant Adeno-Associated Viral (rAAV) vectors to meet rising clinical demand remains a major hurdle. One of the most significant challenges is the generation of large amounts of empty capsids without the therapeutic genome. There is no standardized analytical method to accurately quantify the viral genes, and…

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Can I use vg tools to calculate the depth for a bed range file like with samtools depth?

Can I use vg tools to calculate the depth for a bed range file like with samtools depth? 0 Hi, I have some gam files produce by vg call and I want to know the mean/min/max depth for some ranges stored in a bed file. I could surject the gam…

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Non-coding RNA-mediated endothelial-to-mesenchymal transition in human diabetic cardiomyopathy, potential regulation by DNA methylation | Cardiovascular Diabetology

Raghavan S, Vassy JL, Ho Y, Song RJ, Gagnon DR, Cho K, et al. Diabetes mellitus-related all-cause and cardiovascular mortality in a national cohort of adults. J Am Heart Assoc. 2019;8(4): e011295. Article  PubMed  PubMed Central  Google Scholar  Jia G, Whaley-Connell A, Sowers JR. Diabetic cardiomyopathy: a hyperglycaemia—and insulin-resistance-induced heart…

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2023-11-01 | NDAQ:SGMO | Press Release

Announced additional progress towards strategic transformation into neurology-focused genomic medicine company. Focusing resources on proprietary epigenetic regulation therapies treating neurological diseases and novel AAV capsid delivery technologies. Dosed a total of 25 patients in Phase 1/2 STAAR study in Fabry disease, with promising clinical data continuing to emerge. Deferring additional…

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Issues while installing VG

Issues while installing VG 1 Hi, I am trying to install vg on my Mac (M1 Pro) and during the ‘make’ command I am getting the following error: LDFLAGS are -L/usr/local/lib -L/opt/homebrew/lib -L/opt/homebrew/opt/libomp/lib make: *** No rule to make target `lib/libsdsl.a’, needed by `obj/aligner.o’. Stop. I also had the same…

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DNA damage response(DDR): a link between cellular senescence and human cytomegalovirus | Virology Journal

Hayflick L, Moorhead PS. The serial cultivation of human diploid cell strains. Exp Cell Res. 1961;25:585–621. Article  CAS  PubMed  Google Scholar  Hayflick L. THE LIMITED IN VITRO LIFETIME OF HUMAN DIPLOID CELL STRAINS. Exp Cell Res. 1965;37:614–36. Article  CAS  PubMed  Google Scholar  Schmitt CA, Tchkonia T, Niedernhofer LJ, Robbins PD,…

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vg call – Selecting reference path to call on

vg call – Selecting reference path to call on 0 Hi guys A quick and silly question. I’m using vg call to detect variants in data that I’ve mapped to a graph, but I’m wanting to define which reference paths I call on. I can see how this is done:…

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SRP-9001 Fails to Meet Primary End Point in Phase 3 EMBARK Study

Months after the FDA approved Sarepta Therapeutics’ gene therapy SRP-9001 (Elevidys) for the treatment of ambulatory patients with Duchenne muscular dystrophy (DMD), the company has announced topline data from the phase 3 EMBARK study (NCT05096221), a trial aimed to reinforce the agent’s efficacy. Full results from EMBARK are expected to…

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papain family cysteine protease containing protein, maker-scaffold1702_size30647-snap-gene-0.14 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of papain family cysteine protease containing protein vs. L. salmonis genes Match: EMLSAG00000006045 (supercontig:LSalAtl2s:LSalAtl2s327:400616:404607:-1 gene:EMLSAG00000006045 transcript:EMLSAT00000006045 description:”augustus_masked-LSalAtl2s327-processed-gene-4.0″) HSP 1 Score: 590.497 bits (1521), Expect = 0.000e+0Identity = 283/525 (53.90%), Postives = 368/525 (70.10%), Query Frame = 0 Query: 49 GHVARPLGKSPPNFVRDPPPRTTPPAQWLWNNVNETNFLTVSRNQHLPTYCGSCWAHAATSSLSDRIKIARQGAWPDINLAPQVLISCGPGDGCHGGEAGDANAYMHAQGITDETCSIYRARGQDNGLPCSKLEICSTCE—SKCYQPQHFFTYRVDEFHDVEGESNGEQEANMMAEIHHRGPISCGIAVTQALV-NYTGGLFHDKTGAQEIDHDISVVGYGVDEGTQEKYWLIRNSWGTYWGEQGFFRLIRGVNNLGIESGTCSWATPADTWSDAARE—RAAILSNEITLQKP——LWKQLWTVVADFVDNTRDTDLFRRLKLMQKGCKKLSSPRVPVVNIRPRPQDYVSTADLPEALDWRSVNGTNFLSWSVNQHLPVYCGSCWAQAGLSSLADRFTIADRKRFANLALSVQYILNCQAGGSCHGGDAFPLYAFIQKQGVPDVTCQPYEALDEGPLTDCSKPSKLVCKDCTWPPPEPGQEGNCWAKEKFHRYYVDEYNGVEGADNMKKEILERGPVT 560 GH+ R G+…

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Reduction of retinal ganglion cell death in mouse models of familial dysautonomia using AAV-mediated gene therapy and splicing modulators

Animals All mice were housed in the AALAC-accredited Animal Resource Center at Montana State University. All animal use protocols were approved by the Montana State University Institutional Animal Care and Use Committee (IACUC) (protocol No. 2020-15-IA; Bozeman, MT). The study fulfilled the ARRIVE guidelines, and all experiments complied with relevant…

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need interpretations for the vg call output

need interpretations for the vg call output 0 I successfully obtained the output VCF using the following command: vg call ${gbz_file} \ -k ${pack_file} \ -r ${snarls_file} \ -s ${sample_name} \ -t $SLURM_CPUS_PER_TASK \ -z -a > ${output_vcf_file} I need some interpretations for the VCF data. It appears that the…

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Bi-allelic truncating variants in CASP2 underlie a neurodevelopmental disorder with lissencephaly

Di Donato N, Chiari S, Mirzaa GM, Aldinger K, Parrini E, Olds C, et al. Lissencephaly: expanded imaging and clinical classification. Am J Med Genet A. 2017;173:1473–88. Article  PubMed  PubMed Central  Google Scholar  Guerrini R, Dobyns WB. Malformations of cortical development: clinical features and genetic causes. Lancet Neurol. 2014;13:710–26. Article …

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Excision BioTherapeutics Presents Positive Interim Clinical Data from Ongoing Phase 1/2 Trial of EBT-101 for the Treatment of HIV at ESGCT 30th Annual Congress

Excision BioTherapeutics Excision reported positive safety and biodistribution data to 48 weeks in the first-in-human Phase 1/2 clinical evaluation of EBT-101 No serious adverse events or dose-limiting toxicities were seen in any trial participant EBT-101 was detected in blood in all participants SAN FRANCISCO, Oct. 25, 2023 (GLOBE NEWSWIRE) —…

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Excision BioTherapeutics Presents Positive Interim Clinical

Excision reported positive safety and biodistribution data to 48 weeks in the first-in-human Phase 1/2 clinical evaluation of EBT-101 No serious adverse events or dose-limiting toxicities were seen in any trial participant EBT-101 was detected in blood in all participants SAN FRANCISCO, Oct. 25, 2023 (GLOBE NEWSWIRE) — Excision BioTherapeutics,…

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Vg tools – variant length

Vg tools – variant length 0 Hello, I would like to use vg tools to map short reads Illumina sequencing data and call genotypes of given variants (I have a reference genome and a set of variants detected from long reads). I was wondering, whether there is some length limitation…

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vg call problem request

vg call problem request 0 Hello, recently I’m genotyping some SVs using illumila data, however, I have met some problems that I can not figure it out. The questions are as follows: For some large DEL SVs, for example, SV length > 1kb, the variants will be filtered in the…

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vg call coverage/suppport

vg call coverage/suppport 0 Hello, I am using vg 1.48.0 to try and calculate SV frequencies from short-read poolseq data mapped to a pangenome using giraffe. I was wondering about how the read depth for the reference vs alternate allele is calculated in vg call – is it the (total…

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Clinical characteristics of severe COVID-19 patients

Introduction Coronavirus disease 2019 (COVID-19) first broke out in Wuhan, China, in December 2019. Subsequently, COVID-19 spread rapidly and widely, causing a pandemic.1 It has emerged as a well-known human pandemic over the last three years due to its high pathogenicity and infectivity, which posed serious risks to public health.2…

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Lack of correspondance of GFA node IDs to giraffe/call node IDs

I have a GFA graph built with PGGB using several samples. I want to genotype some other samples with short reads using VG Giraffe. After investigating how to generate the corresponding indexes for VG Giraffe from a GFA generated with PGGB, I think I have found a way to do…

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Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance

Challenges in Variant Calling and Genotyping with Short-Read Data Mapped to a Pangenome Graph: Seeking Guidance 0 Hello all, We are reaching out since we have some practical questions regarding variant calling and analyses of short-read data mapped to a pangenome graph. We are working on a project aimed to…

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Mitigating a TDP-43 proteinopathy by concentrating on ataxin-2 utilizing

Concentrating on ataxin-2 with RfxCas13d Due to its potential to affect TDP-43-associated toxicity20,25,26, ataxin-2 has emerged as a doubtlessly broadly relevant goal for ALS-FTD, as TDP-43 pathology is noticed in ~97% of ALS instances1,4,5 and ~45% FTD occurrences1,2,4. Given this, we sought to find out if RNA-targeting CRISPR effector proteins…

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Interpretation question regarding vg call result vcf

Thank you so much for creating such an amazing tool. I am currently having difficulty interpreting vcf results from vg call. I currently performed haplotype-resolved genome assembly and created a graph-genome using both haplotypes (HA and HB) via pggb and vg. Afterwards, a variant called vcf was completed through vg…

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VG autoindex with pangenome constructed using minigraph-cactus

Dear developers, I am trying to construct a reference pangenome of a fungi species. After successfully constructing my pangenome using minigraph-cactus, I am struggling to add my isolates’ annotations. For some background: We have de novo assembled and annotated 11 isolates and used the current reference (which has a chromosomal…

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HiFi read alignment with vg giraffe

HiFi read alignment with vg giraffe 0 Hi, I used vg giraffe to align long read hifi sequences to a pangenome using vg giraffe and these are the numbers i am getting by running vg stats. Total alignments: 4144653 Total primary: 4144653 Total secondary: 0 Total aligned: 4144644 Total perfect:…

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Bugs : systemd package : Ubuntu

tests-in-lxd seems to fail to download the lxd image used for the test (or something similar), looking at the log:…Publishing instance: Image pack: 85% (5.51MB/s) Instance published with fingerprint: 83b511be44395f2afc7d4d1ee0708cb18834c8b15cb208c9d218964ed84791146845s autopkgtest [09:11:14]: starting date and time: 2023-10-03 09:11:14+00006845s autopkgtest [09:11:14]: version 5.28ubuntu16845s autopkgtest [09:11:14]: host autopkgtest; command line: /usr/bin/autopkgtest -U…

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Analysing short reads mapped to a pangenome graph

Analysing short reads mapped to a pangenome graph 0 Hello all, Research that I am working on requires me to identify organisms and specific genetic information that these organisms carry. The way I do this, is by first constructing a pangenome graph of several other organisms, to capture most of…

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Pangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits

Swingle, W. T. & Reece, P. C. In The Citrus Industry, History, World Distribution, Botany, and Varieties, Vol. 1 (eds Reuther, W. et al.) 190–143 (Univ. of California Press, 1967). Morton, C. M. & Telmer, C. New subfamily classification for the Rutaceae. Ann. Mo. Bot. Gard. 99, 620–641 (2014). Article …

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Identifying ESR1 Mutations to Determine Resistance in HR+ Metastatic Breast Cancer

The global disease burden of breast cancer (BC) is a serious health concern worldwide, especially among women. Globally, about 2.3 million women were diagnosed with BC in 2020, and there were 685,000 deaths from BC.1 Various BC subtypes have been identified based on the expression of genes encoding hormone receptors…

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Bug of vg surject

Bug of vg surject 0 Hello I tried to use vg surject to convert gam to bam, there was a problem here. If i generate the bam from giraffe by parameter ‘-o bam’, the size of bam file is more bigger than bam generated from vg surject. And then, using…

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Identify parent of each read in a GAF

Identify parent of each read in a GAF 0 I have a .gfa created by running the fasta files of two genomes through the Cactus-Minigraph pipeline. I am aligning PacBio Hifi reads to that reference using GraphAligner. Column 6 of the resulting GAF file lists the segments for the alignment…

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vg rna pantranscriptome

vg rna pantranscriptome 0 Hello,VG team. I have assembled my pan-transcriptome according to this technical route. Is this approach feasible if I build a Haplotype-aware pantranscriptome using the pan-transcriptome and a haplotype vcf file generated by standard reference genome ? It is known that these transcripts generated from unmap-reads that…

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hypothetical protein LOTGIDRAFT_112989, maker-scaffold299_size217019-snap-gene-1.29 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of hypothetical protein LOTGIDRAFT_112989 vs. L. salmonis genes Match: EMLSAG00000011196 (supercontig:LSalAtl2s:LSalAtl2s761:366436:368626:1 gene:EMLSAG00000011196 transcript:EMLSAT00000011196 description:”maker-LSalAtl2s761-augustus-gene-2.9″) HSP 1 Score: 208.764 bits (530), Expect = 1.424e-65Identity = 100/171 (58.48%), Postives = 126/171 (73.68%), Query Frame = 0 Query: 120 NPIVFFDITIGGDPVGRIVMELYANVVPKTVDNFRALCTGEKGQVGGSGIPLHYKNSSFHRVINRFMLQGGDFTAGDGTGGASIYGEKFADENFLLKHEKPGLLSMANAGPGTNGSQFFLTTVNCPHLDGKHVVFGRAIKGMGIVNEIEVMETT-SDKPNVEVKIADCGQI 289 NP+VFFDI +G +GRIVMEL+A+V PKT +NFR CTGE…

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How to change the output reference for vg giraffe BAM output

How to change the output reference for vg giraffe BAM output 1 I constructed a pan genome graph with mingraph cactus with two reference genomes specified. I am trying to align reads to the graph and produce a BAM file that is specific to one of the references. How can…

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Can vg stats -a be used on a bam file?

It requires graph format, not BAM: $ ./vg stats usage: ./vg stats [options] [<graph file>] options: -z, –size size of graph -N, –node-count number of nodes in graph -E, –edge-count number of edges in graph -l, –length length of sequences in graph -L, –self-loops number of self-loops -s, –subgraphs describe…

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Complete-genome sequencing and comparative genomic characterization of blaNDM-5 carrying Citrobacter freundii isolates from a patient with multiple infections | BMC Genomics

Sheu CC, Chang YT, Lin SY, Chen YH, Hsueh PR. Infections Caused by Carbapenem-Resistant Enterobacteriaceae: An Update on Therapeutic Options. Front Microbiol. 2019;10:80. Article  PubMed  PubMed Central  Google Scholar  HammoudiHalat D, Ayoub Moubareck C. The Current Burden of Carbapenemases: Review of Significant Properties and Dissemination among Gram-Negative Bacteria. Antibiotics (Basel)….

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The cGAS-STING-YY1 axis accelerates progression of neurodegeneration in a mouse model of Parkinson’s disease via LCN2-dependent astrocyte senescence

doi: 10.1038/s41418-023-01216-y. Online ahead of print. Affiliations Expand Affiliations 1 Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu, 211166, PR China. 2 Jiangsu Key Laboratory of Neurodegeneration, Department of Pharmacology, Nanjing Medical University, 101 Longmian Avenue, Nanjing, Jiangsu, 211166, PR China. drh@njmu.edu.cn….

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Using vg gamsort with naive sorting algorithm

Hello, I am currently using VG to map reads to a graph I made (using a HPC), and I’m having issues when sorting the ouput gam: vg gamsort \ -p \ ${filename}_mapped.gam > ${filename}_mapped.sorted.gam break into sorted chunks [ ] 0.0%^M break into sorted chunks [= ] 1.1%^M break into…

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vg tools is running, but memory consumption is not happened and log files are not updated

vg tools is running, but memory consumption is not happened and log files are not updated 2 Hi there, I use vg tools for giraffe mapping. I started vg tools 2022.01.13 and now(2022.01.17). vg makes log files : chunked fasta, chunked vcf file, etc… I has checked log files. log…

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VG mapping paired-end reads: error [xg]: multiple hits for XXX

Hi everyone, I did create my first graph using vcf from HGDP as follow: vg construct -r ref.fa -v sub-chrXX.vcf.gz > pXX.vg vg ids -j $(for i in $(seq 1 22); do echo p${i}.vg; done) vg index -x all.xg $(for i in $(seq 1 22); do echo p${i}.vg; done) vg…

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VG node not present in graph

Hello everyone, I’m currently working on constructing my first pangenome using VG and could use some help. My approach involves using VCF files from individuals in HGDP and following the steps outlined on their GitHub tutorial: GitHub Tutorial Link. This tutorial fits my needs but wasn’t updated since 2020 …..

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display vcf after giraffe alignment on IGV

display vcf after giraffe alignment on IGV 0 I performed Giraffe alignment to map reads to the HPRC pangenome, resulting in a gam file. Subsequently, I utilized the following commands to generate a .vcf file: Generated a pack file with the following command: ./vg pack –x hprc-v1.0-mc-grch38-minaf.0.1.gbz –g hprc1004mapped.gam >…

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The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph

The number of SVs called by `vg call` is much smaller than the number of SVs in the VCF used to construct the graph 0 My objective is to identify the structural variations (SVs) located on chromosome NC_058090.1. The reason for solely focusing on a single chromosome is due to…

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Comparing SV calls produced by VG call on a Minigraph-Cactus produced Pangenome Graph vs. a linear reference

Comparing SV calls produced by VG call on a Minigraph-Cactus produced Pangenome Graph vs. a linear reference 0 I’m presently working on generating structural variant (SV) calls using vg call. I constructed the graph using whole genome assemblies using Minigraph-Cactus (MC), and aligned short-read data using vg giraffe. I would…

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AAV-mediated base-editing therapy ameliorates the disease phenotypes in a mouse model of retinitis pigmentosa

Ethics statement This study did not involve human data. All animal procedures were approved by the Institutional Review Board of Shanghai Jiao Tong University and were conducted in accordance with the Association for Research in Vision and Ophthalmology Statement for the Use of Animals in Ophthalmic and Visual Research. Animals…

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creating vcf file after giraffe alignment

creating vcf file after giraffe alignment 0 I am using the HPRC human pangenome as a reference for aligning my whole genome sequencing data. My focus is on the HLA region, and I anticipate improved alignment results using the pangenome reference. To achieve this, I make use of the provided…

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how to compare mapping of WES samples to human pangenome?

how to compare mapping of WES samples to human pangenome? 0 Hi, I’m still trying to wrap my head around the new human pangenome reference and would like some advice on how to go about analyzing some of the WES (hg38/hg19 baits) that I currently have. How should I calculate…

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How to identify which genome the variations in the pan-genome graph originate from

How to identify which genome the variations in the pan-genome graph originate from 1 We want to use vg to construct a pan-genome. In order to detect variations in the subsequent pan-genome graph and determine which genomes they exist in, we intend to retain the genome source information for the…

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why does vg convert doesn’t work?

why does vg convert doesn’t work? 1 I am using vg version 1.49.0 on Ubuntu I am trying to convert a gam file to a gfa format and it is not working. I have the file hprc1004mapped.gam and I run the command: ./vg convert –G hprc1004mapped.gam > hprc1004mapped.gfa And I…

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Voyager Therapeutics Reports Second Quarter 2023 Financial and Operating Results

– Introduced new vectorized anti-Aβ antibody gene therapy research initiative, expanding Alzheimer’s disease portfolio – – Executed license agreement with Sangamo for prion disease treatment – – Presented validating preclinical results including increased brain transduction of IV-administered TRACER™ capsids across multiple non-human primate species at ASGCT 2023 – – Conference…

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Nextflow files not referenced correctly when using wildcard in a for loop

Hi, I’m having some problems with my nextflow workflow when I use wildcards (*) to call in files. The files are created fine, (using process augment below) but when it is used by process snarls, it calls them as follows: CH-A2504_1.aug.gam -> workdir/2c/ce66a6417872a428111b7c2a5995d4/CH-A2504_01.aug.gam CH-A2504_1.aug.pg -> workdir/2c/ce66a6417872a428111b7c2a5995d4/CH-A2504_01.aug.pg … … CH-A2504_23.aug.gam ->…

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giraffe error “libgomp: Thread creation failed: Operation not permitted”

giraffe error “libgomp: Thread creation failed: Operation not permitted” 0 I am working with vg version 1.49.0 and I am trying to run giraffe alignment. when I run the giraffe command on a dxjupyterlab terminal, get the following error message: libgomp: Thread creation failed: Operation not permitted this error also…

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Reply to: Re-evaluating evidence for adaptive mutation rate variation

replying to L. Wang et al. Nature doi.org/10.1038/s41586-023-06314-y (2023) Wang and colleagues1 argue that our report2 of lower mutation rates in gene bodies, essential genes and regions marked by H3K4me1 must result from DNA sequencing errors. We appreciate the issues raised by them and by other colleagues3. Although we overlooked…

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SV calling using giraffe/vg

SV calling using giraffe/vg 0 It’s not very clear to me how exactly VG or Giraffe carries out SV calling (if it truly does). The tutorials mention how we can do genotyping using existing SV calls, but I was wondering if VG or Giraffe can actually identify novel SVs in…

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Substantial reduction in read mapping following VG surject

Substantial reduction in read mapping following VG surject 0 I did a small comparison of total mapping of a small short-read dataset to: a graph constructed using cactus-minigraph composed of eight whole genome alignments using VG giraffe the same cactus-minigraph graph, but indexed using VG and mapped to with VG…

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vg giraffe unavailable perf events issue

vg giraffe unavailable perf events issue 0 Hi, I’m trying to map WGS reads to genome graph using vg giraffe. And I got a warning related to “perf events” while mapping reads. Can I ignore this warning? Here is the log for my execution. Preparing Indexes Loading Minimizer Index Loading…

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Indexing the human pangenome draft

Indexing the human pangenome draft 0 Hi, I am attempting to create a VG index against the human pangenome draft using vg autoindex. Here is the command: vg autoindex –gfa hprc-v1.0-mc-grch38-minaf.0.1.gfa –tmp-dir /home/ec2-user/pangenome/tmp vg has been running for about a week now and I’ve seen the following in the logs…

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using vg on DNA-nexus platform

using vg on DNA-nexus platform 0 I have data stored on the DNA-Nexus cloud service and I would like to utilize the vg tool, particularly the giraffe alignment tool, with this data. I attempted to open a dxjupiterlab environment and used the terminal to install vg. However, after installation, the…

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vg get started tutorial

vg get started tutorial 0 Are there any tutorials or recommended YouTube channels that can assist me in getting started with vg? vg. beginners offtopic • 25 views • link updated 13 minutes ago by Michael 52k • written 2 hours ago by Michal • 0 Login before adding your…

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population-level stratagy of vg call

population-level stratagy of vg call 0 Hello VG Team, I have been contemplating whether there is a more efficient approach to perform population-level Structural Variants (SVs) calling using the VG calling pipeline. Based on my understanding, the VG calling pipeline consists of the following steps: 1) vg construct to create…

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VG Giraffe multi-mapped reads and definition for MAPQ score

VG Giraffe multi-mapped reads and definition for MAPQ score 0 Hi, I am recently playing with VG giraffe. The tool is amazing. I want to say thank you for the developers of VG team. I do have 2 little questions regarding the alignment. What is the definition of MAPQ (mapping…

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vg map time consuming

vg map time consuming 1 Hi vg team, The vg map command has been running for 4 days. Initially, the size of the .gam file accumulated to around 100G, but then suddenly dropped to 1G. Currently, the size is around 2.3G and it continues to increase. The command used is…

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build error with vg tools

build error with vg tools 0 I am trying to use vg tools on my AWS Ubuntu server and it won’t compile. I followed the instructions listed here but when I get to the point where I need to build with . ./source_me.sh && make it gives me this error:…

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Comment: unable to find most of SVs in constructed graph.vg

Thank you for your response. I still have some questions regarding Giraffe. In my case, the `input.vcf` file is unphased and contains numerous structural variations (SVs), which means that overlaps between SVs are quite common. According to the guide [Mapping short reads with Giraffe](https://github.com/vgteam/vg/wiki/Mapping-short-reads-with-Giraffe), using Giraffe for mapping might not…

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unable to find most of SVs in constructed graph.vg

Hi vg team, I followed the instructions provided in the [Working with a whole genome variation graph](https://github.com/vgteam/vg/wiki/Working-with-a-whole-genome-variation-graph) to construct my own variation graph. After constructing the graph, I wanted to validate if my `input.vcf` file successfully passed all the structural variations (SVs) to the graph. My approach was to use…

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Construct a pantranscriptome reference with two haplotypes from a single sample.

Construct a pantranscriptome reference with two haplotypes from a single sample. 0 Hello, I am trying to construct a graph reference for rpvg using two haplotypes from a single sample. I created a GFA file from two haplotype from single sample with pggb. Then, I generated VCF file and graph.pg…

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FDA Greenlights Gene Therapy Roctavian for Severe Hemophilia A

The Food and Drug Administration (FDA) has approved Roctavian™ (valoctocogene roxaparvovec-rvox) for the treatment of adults with severe hemophilia A (congenital factor VIII [FVIII] deficiency with FVIII activity < 1 IU/dL) without preexisting antibodies to adeno-associated virus serotype 5 (AAV5) detected by an FDA-approved test. Administered as a single-dose infusion,…

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FDA Accepts Pfizer’s Application for Hemophilia B Gene Therapy Fidanacogene Elaparvovec

NEW YORK, June 27, 2023–(BUSINESS WIRE)–Pfizer Inc. (NYSE: PFE) announced today that the U.S. Food and Drug Administration (FDA) has accepted the company’s Biologics License Application (BLA) for fidanacogene elaparvovec for the treatment of adults with hemophilia B. In parallel, the European marketing authorization application (MAA) for fidanacogene elaparvovec has…

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Comment: warning[vg::Watchdog]

Thank you for your replay! No error was eventually reported because the command didn’t end up running through. I run this conmand **vg giraffe -t 24 -Z 63-pg.d2.gbz -d 63-pg.d2.dist -m 63-pg.d2.min -f IRIS_313-7684_1.QC.fastq.gz -f IRIS_313-7684_2.QC.fastq.gz > IRIS_313-7684_mapped.gam** When I first started running this command, the size of the **gam**…

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warning[vg::Watchdog]

**I am trying to use giraffe to map paried-end short-reads against my pan-genoome graph,I met some warning(below). Could you tell me how I can do ?** warning[vg::Watchdog]: Thread 16 has been checked in for 10 seconds processing: ERR626576.4149, ERR626576.4149 warning[vg::Watchdog]: Thread 17 has been checked in for 10 seconds processing:…

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Retrieving alignment scores with vg surject

Retrieving alignment scores with vg surject 0 Hello! I’m trying to get multiple alignments with their corresponding alignment scores for paired-end reads against a pangenome using vg giraffe, and then vg surject to convert gam to bam. As result, the generated bam file contains multiple alignments for paired-end reads but…

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vg convert does not preserve the order of the reads

vg convert does not preserve the order of the reads 0 When I use vg convert (v.1.39) to convert a gam file to a gaf file (or vice versa), I find that the order of the reads will not be preserved. For example, when I sort the reads according to…

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Very few snp and indels variation were identified using PAV variation input file base on vg call

Very few snp and indels variation were identified using PAV variation input file base on vg call 0 Hi all, We want to find the snp and indels variation from the result vcf file BS_graph_call.vcf by using the pan_genome vg analysis software. There are only **fewer than 20 snp and…

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Reduce set of chromosomes in Pangenome graph

Reduce set of chromosomes in Pangenome graph 0 Hi, I was wondering if it is possible with vg to reduce the set of chromosomes in the pangenome graph. It would be analogous to reducing the set of chromosomes in your conventional linear genome reference to be able to do less…

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Whole genome sequencing of Salmonella enterica serovars isolated from humans, animals, and the environment in Lagos, Nigeria | BMC Microbiology

Crump JA, Luby SP, Mintz ED. The global burden of typhoid fever. Bull World Health Organ. 2004;82(5):346–53. PubMed  PubMed Central  Google Scholar  Braden CR. Salmonella enterica serotype Enteritidis and eggs: a national epidemic in the United States. Clin Infect Dis. 2006;43:512–7. Article  PubMed  Google Scholar  Rotimi V, Jamal W, Pal…

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BAM creation – vg surject vs vg mpmap output

BAM creation – vg surject vs vg mpmap output 1 I have a graph that I am mapping RNA seq reads to and I want to create a BAM for a comparison study. Is there any difference between using vg surject, and selecting BAM as the output format when using…

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A New AI Research From Google Declares The Completion of The First Human Pangenome Reference

Researchers have spent decades piecing together a human genome map, a comprehensive copy of each individual’s genetic instructions. In 2000, researchers completed the first draft, but it needed key components. After completing the reference genome in 2022, they still had a ways to go. Genomics has spent the past three…

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CRISPR Regulatory Landscape Interpreting FDA’s Gene Editing Guidance for Clinical-Grade sgRNA

In this webinar, Synthego’s Senior Director of Quality & Regulatory, Beckinam Nowatzke, and Senior Regulatory Specialist Lina Jamis will elaborate on Synthego’s preclinical offerings in support of CRISPR therapy developers and an interpretation of FDA’s expectations for CRISPR gene editing components.   What will you learn: Health authority expectations for…

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Mapping fewer reads to a genome graph than a linear reference

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…

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Gene expression in African Americans, Puerto Ricans and Mexican Americans reveals ancestry-specific patterns of genetic architecture

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…

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The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae

Elston KM, Leonard SP, Geng P, Bialik SB, Robinson E, Barrick JE. Engineering insects from the endosymbiont out. Trends Microbiol. 2022;30:79–96. Article  CAS  PubMed  Google Scholar  Brophy JAN, Triassi AJ, Adams BL, Renberg RL, Stratis-Cullum DN, Grossman AD, et al. Engineered integrative and conjugative elements for efficient and inducible DNA…

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What is the node_id in vg giraffe output (gaf or gam)?

What is the node_id in vg giraffe output (gaf or gam)? 0 Hi, I am playing with the genome graph I built from 2 different individual whole genome sequencing data. Also, I generated 1 million simulated reads. However, while I tried to map the simulated read back to the genome…

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how can I generate a VCF (in hg38 coords) of differences between hg38 and CHM13?

I downloaded s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz which contains hg38, chm13, and other assemblies, and now am trying to use vg to generate a VCF with the variants in CHM13 relative to hg38. After converting to vg format, by running vg convert <(gunzip -c hprc-v1.0-minigraph-grch38.gfa.gz) > hprc-v1.0-minigraph-grch38.vg, I tried a few different variations of…

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Comparison of survival outcomes of different treatment modalities for patients with primary splenic diffuse large B cell lymphoma

Pan X, Ren D, Li Y, Zhao J (2021) The effect of surgery on primary splenic lymphoma: a study based on SEER database. Cancer Med (20):7060–7070 Yu SC, Lin CW (2013) Early-stage splenic diffuse large B-cell lymphoma is highly associated with hepatitis C virus infection. Kaohsiung J Med Sci 29(3):150–156…

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r – GGplot: Line in stat_summary is not being displayed

I am trying to have a graph showing a line connecting the dots of each group in each variable. However it seems like ggplot refuses to render the line and I am not sure why. Here is the code: ggplot(DF_Compound, aes(color=MainThemes, y=value, x=Variable)) + stat_summary( fun.y=”mean”, geom=”point”, size=2, ) +…

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CRISPR/Cas13d-Mediated Mutant Huntingtin Elimination

Huntington’s disease (HD) is a late-onset, fatal neurodegenerative disorder with no cure; currently available treatments merely provide modest relief of symptoms. HD is caused by a gain-of-function mutation: a trinucleotide repeat hyperexpansion in the first intron of the HTT gene, which codes for the Huntingtin protein. Spearheaded by collaborators Dr….

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