Tag: STAR

genetic epidemiology postdoc

Qualification Details. Objective/methods: This report investigates by histology, immunohistochemistry and in situ hybridization the histological and . Philip Lupo, Ph.D. Dr. Lupo is a co-principal investigator in the Systems Epidemiology of Cancer Training Program and an associate professor in the Section of Hematology-Oncology in the Department of Pediatrics. . «Genetic…

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A*STAR – Agency for Science, Technology and Research hiring Bioinformatics Specialis, Laboratory of Systems Biology & Data Analytics, GIS in Singapore, Singapore

 The Genome Institute of Singapore (GIS) is an institute of the Agency for Science, Technology and Research (A*STAR). It has a global vision that seeks to use genomic sciences to achieve extraordinary improvements in human health and public prosperity. GIS is dedicated to creating a social culture that is…

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nf-core presentation – HackMD

<!– .slide: data-background=”raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg&#8221; –> <a href=”nf-co.re”><img src=”raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-darkbg.svg&#8221; width=”60%”></img></a> # What is nf-core\? [Maxime U Garcia](https://maxulysse.github.io/) ▸ [<i class=”fa fa-twitter” aria-hidden=”true”></i>@gau](https://twitter.com/gau/) | [<i class=”fa fa-github” aria-hidden=”true”></i>@maxulysse](https://github.com/maxulysse/) [Karolinska Institutet](https://ki.se/) | [Science for Life Laboratory](https://www.scilifelab.se/) Sweden — ## Overview – 🗄️ [Barntumörbanken](https://ki.se/forskning/barntumorbanken/) – 🧬 [NGI](https://ngisweden.scilifelab.se/) – 🍬 [Nextflow](https://www.nextflow.io/) – 🧙 [nf-core](https://nf-co.re/) — ##…

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Multiplexed genome regulation in vivo with hyper-efficient Cas12a

. 2022 Apr;24(4):590-600. doi: 10.1038/s41556-022-00870-7. Epub 2022 Apr 12. Lucie Y Guo #  1   2 , Jing Bian #  3 , Alexander E Davis  4 , Pingting Liu  4 , Hannah R Kempton  3 , Xiaowei Zhang  3 , Augustine Chemparathy  3 , Baokun Gu  3 , Xueqiu Lin  3 , Draven A Rane  3 , Xiaoshu Xu  3 , Ryan M…

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On a reference pan-genome model (Part II)

12 July 2019 I wrote a blog post on a potential reference pan-genome model. I had more thoughts in my mind. I didn’t write about them because they are immature. Nonetheless, a few readers raised questions related to my immature thoughts, so I decide to add this “Part II” as…

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New NSCC Singapore Collaborations to Develop HPC-Enabled Bioinformatics Capabilities

Singapore, April 22, 2022 — Two collaborations were signed today between APBioNET and NSCC as well as between AMBIS and NSCC to strengthen cooperation to develop and upskill the field of bioinformatics in Singapore. The proposed activities include developing high-performance computing (HPC) capability and talent development for bioinformatics, education and…

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GDCprepare of RNAseq counts produces error

GDCprepare of RNAseq counts produces error 1 @76ac7b25 Last seen 12 minutes ago Canada Hello everyone! I have been using the TCGAbiolinks package for the last couple years to access RNAseq data for the TCGA-LAML project. Just very recently, I had noticed that I could no longer use GDCquery to…

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Nanopore sequencing of the pharmacogene CYP2D6 allows simultaneous haplotyping and detection of duplications.

Liau Y et al. Pharmacogenomics. 2019 Sep; 20(14):1033-1047 doi.org/10.2217/pgs-2019-0080PMID: 31559921 Show Details AbstractAuthors Aim: Long read sequencing offers the promise of overcoming some of the challenges in accurate genotyping of complex genes, along with the advantage of straightforward variant phasing. We have established methods for sequencing and haplotyping of the…

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HTSeq Counts no longer available

HTSeq Counts no longer available 1 @vm-21340 Last seen 8 hours ago Brazil I’m working with breast cancer expression data from the TCGA-BRCA project. All my scripts were written to retrieve HTSeq counts from GDC, but they seem to have been removed from the GDC Data Portal. When using GDCquery,…

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Comparative genomic analysis of vertebrate mitochondrial reveals a differential of rearrangements rate between taxonomic class

Pereira, S. L. Mitochondrial genome organization and vertebrate phylogenetics. Genet. Mol. Biol. 23, 745–752 (2000). CAS  Google Scholar  Boore, J. L. Animal mitochondrial genomes. Nucl. Acids Res. 27, 1767–1780 (1999). CAS  PubMed  PubMed Central  Google Scholar  Formenti, G. et al. Complete vertebrate mitogenomes reveal widespread gene duplications and repeats. BioRxiv…

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Accurate assembly of multi-end RNA-seq data with Scallop2

Trapnell, C. et al. Transcript assembly and quantification by RNA-seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat. Biotechnol. 28, 511–515 (2010). Article  Google Scholar  Guttman, M. et al. Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat. Biotechnol. 28,…

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Untangling SNP Variations within CYP2D6 Gene in Croatian Roma

CYP2D6 is a highly polymorphic gene whose variations affect its enzyme activity. To assess whether the specific population history of Roma, characterized by constant migrations and endogamy, influenced the distribution of alleles and thus phenotypes, the CYP2D6 gene was sequenced using NGS (Next Generation Sequencing) method-targeted sequencing in three groups…

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New Image Shows Mysterious ‘Odd Radius Circles’ in Space

Mystery of space would be about to be deciphered 0:53 (CNN) — There’s a mysterious new kind of object in space, and after capturing their best image to date, astronomers are one step closer to understanding these strange celestial balls. They are known as odd radius circles (ORC). Though thinking…

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AAV-delivered suppressor tRNA overcomes a nonsense mutation in mice

Wang, D., Tai, P. W. L. & Gao, G. Adeno-associated virus vector as a platform for gene therapy delivery. Nat. Rev. Drug Discov. 18, 358–378 (2019). CAS  PubMed  PubMed Central  Google Scholar  Li, C. & Samulski, R. J. Engineering adeno-associated virus vectors for gene therapy. Nat. Rev. Genet. 21, 255–272…

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rna seq – RNAseq SNP discovery: deciding upon filters and dealing with allele expression bias

I am working with non-model plant RNA samples which we have been deep sequenced and analysed using STAR aligner under default parameters. Aim We would like to conduct SNP discovery of these samples. Objective Our ultimate goal with this genotypic data is to search for variants (both SNPs and indels)…

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Results From Genome Sequencing and Clinical Genotyping.docx

Objective: Hmong individuals represent a unique East Asian subpopulation in whom limited information concerning pharmacogenetic variation exists. The objectives of this study were to comprehensively characterize the highly polymorphic CYP2D6 gene in Hmong, estimate allele and phenotype frequencies and to compare results between two testing platforms. Methods: DNA from 48…

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Mitogenomics provides new insights into the phylogenetic relationships and evolutionary history of deep-sea sea stars (Asteroidea)

Mah, C. L. & Blake, D. B. Global diversity and phylogeny of the asteroidea (Echinodermata). PLoS ONE 7, e35644. doi.org/10.1371/journal.pone.0035644 (2012). ADS  CAS  Article  PubMed  PubMed Central  Google Scholar  WoRMS. Asteroidea. Accessed at: www.marinespecies.org/aphia.php?p=taxdetails&id=123080. on 2021-08-02. Blake, D. B. Adaptive zones of the class Asteroidea (Echinodermata). Bull. Mar. Sci. 46,…

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Low transcript quantification with Salmon using GRCm39 annotations

Hi everyone, first time working with mouse samples and unfortunately, there are fewer resources available for the latest mouse Ensembl genome than I was expecting. What I’ve done: I performed rRNA depletion on total RNA extracted from mouse tissue and created Illumina libraries using a cDNA synthesis kit with random…

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A single-cell atlas of human and mouse white adipose tissue

Rosen, E. D. & Spiegelman, B. M. What we talk about when we talk about fat. Cell 156, 20–44 (2014). CAS  PubMed  PubMed Central  Google Scholar  Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006)….

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Mitogenome of a stink worm (Annelida: Travisiidae) includes degenerate group II intron that is also found in five congeneric species

Tan, M. H. et al. Comparative mitogenomics of the Decapoda reveals evolutionary heterogeneity in architecture and composition. Sci. Rep. 9, 1–16 (2019). ADS  Google Scholar  Zhang, Y. et al. Phylogeny, evolution and mitochondrial gene order rearrangement in scale worms (Aphroditiformia, Annelida). Mol. Phylogenet. Evol. 125, 220–231 (2018). CAS  PubMed  Google…

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Next Generation Sequencing (NGS) Leader Nick McCooke Joins Genomics Company RevoluGen as Strategic Advisor

LONDON, March 10, 2022–(BUSINESS WIRE)–UK genomics company, RevoluGen Ltd. (RevoluGen or the Company), today announces that Nick McCooke, widely recognised leader in the next generation sequencing (NGS) field, has been appointed as Strategic Advisor. This press release features multimedia. View the full release here: www.businesswire.com/news/home/20220310005076/en/ Nick McCooke, NGS Expert and…

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Top 17 b cell lymphoma treatment in 2022

Below are the best information and knowledge on the subject b cell lymphoma treatment compiled and compiled by our own team tuhoangkaido: 1. Treating B-Cell Non-Hodgkin Lymphoma 2. Treatments for B-Cell Lymphoma 3. Diffuse Large B-Cell Lymphoma: Treatment Options 4. B-cell Lymphoma 5. B-cell Lymphoma: Types, Symptoms & Prognosis 6….

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Galaxy Genome [Space Sim] HACK/MOD Unlocked All vVaries with device

Download Galaxy Genome [Space Sim] Mod Varies with device for android apk & iphone ios 4.4 and up Galaxy Genome is an open world sci-fi space simulator. You can upgrade your ship and customize each component as you hunt, explore, fight, mine, smuggle, trade and survive in a brutal galaxy….

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Research Roundup: New Insights into Alzheimer’s, ALS and FTD

BSIP/UIG Via Getty Images One particular gene variant, APOE4, is associated with an increased risk of Alzheimer’s disease. But why that is the case, what the mechanism of action is, has eluded researchers. At least one pathway has been determined, and it has possible repercussions in developing therapies against the…

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How to extract fasta sequences from assembled transcripts generated by Stringtie

How to extract fasta sequences from assembled transcripts generated by Stringtie 4 Hi all, I used STAR and stringtie for mapping reads to reference genome and assembly. As you know, the generated assembled transcripts by stringtie are in gtf format. Now, I want to have fasta sequence of assembled transcript….

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HRJOB7442 Bioinformatics Scientist 2 (Various Locations) in Nether Alderley, Macclesfield (SK10) | Almac Group (Uk) Ltd

Bioinformatics Scientist 2 Hours: 37.5 hours per week Salary: Competitive Ref No: HRJOB7442 Business Unit: Diagnostic Services Location: Craigavon or Manchester Open To: Internal and External Applicants The Company Almac Diagnostic Services is a leading stratified medicine business, specialising in biomarker-driven clinical trials. We are incredibly proud to be involved…

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Aaron Rodgers apologises to Shailene Woodley amid break-up rumours

NFL Player Aaron Rodgers has recently spoken in length about his relationship with actor Shailene Woodley, addressing how criticism of his COVID-19 vaccination status has affected his loved ones. According to The Hollywood Reporter, both stars confirmed their engagement last year, although some media outlets recently reported that the…

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use tcgabiolinks package to download TCGA data

TCGA Data download in terms of ease of use ,RTCGA The bag should be better , And because it’s already downloaded data , The use is relatively stable . But also because of the downloaded data , There is no guarantee that the data is new .TCGAbiolinks The package is…

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Difference of results with the same input [RNAseq analysis]

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

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What Is The Difference Between Dgp And Ddgtp?

DIG stands for Deputy Inspector General. It is a one- star rank in the Indian Police Service. This is a senior rank than Senior Superintendent of Police (SSP) or Deputy Commissioner of Police (DCP). An officer holding this position works under the Inspector General of Police (IG) or Joint Commissioner…

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ATF7ip Targets Transposable Elements for H3K9me3 Deposition to Modify CD8+ T Cell Effector and Memory Responses

Key Points ATF7ip is a critical regulator of CD8+ T cell effector and memory responses. Deletion of ATF7ip in CD8+ T cells results in enhanced Il2 and Il7r expression. ATF7ip targets transposable elements to modulate Il7r and Il2 expression. Abstract CD8+ T cells are critical for the immune response to…

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Astronomers close in on new way to detect gravitational waves

Supermassive black holes orbiting each other very closely are expected to produce gravitational waves.Credit: NASA’s Goddard Space Flight Center/Science Photo Library Astronomers could be on the verge of detecting gravitational waves from distant supermassive black holes — millions or even billions of times larger than the black holes spotted so…

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Surgical Techniques to Optimize Ovarian Reserve during Laparoscopic Cystectomy for Ovarian Endometrioma

This protocol presents techniques to laparoscopically excise ovarian endometrioma, to perform adhesiolysis with sparing electrosurgical application, and to employ intraoperative chromopertubation to assess for genital tract patency. This systematic approach will facilitate optimal endometriosis management, guide concomitant adnexal surgeries, and enhance post-surgical fertility outcomes. Surgical techniques to optimize ovarian reserve…

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CRISPR-Cas12a ribonucleoprotein-mediated gene editing in the plant pathogenic fungus Magnaporthe oryzae

. 2021 Dec 24;3(1):101072. doi: 10.1016/j.xpro.2021.101072. eCollection 2022 Mar 18. Affiliations Expand Affiliation 1 Department of Plant Pathology, Kansas State University, Manhattan, KS, USA. Free PMC article Item in Clipboard Jun Huang et al. STAR Protoc. 2021. Free PMC article Show details Display options Display options Format AbstractPubMedPMID . 2021 Dec…

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MARS seq alingment

MARS seq alingment 0 Hello everyone, new here and also new to the field. was asked to create a pipeline for RNA seq and after two months of self learning of how to interact with each code im stuck with the program STAR. what im trying to do for now…

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RNAseq using galaxy

RNAseq using galaxy 0 @e3a40d42 Last seen 1 hour ago United States I am new to rnaseq, I am using RNA star to map the genes and count reads per gene. After running the feature counts on RNA Star output, I will like to proceed to the deseq2 for differential…

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RNA-seq analysis cloud server

RNA-seq analysis cloud server 1 Hi all, I have some RNA-seq of mice (around 200GB) and I want to perform a RNA-seq analysis (including QC, mapping, quantification, differential expression analysis). But I don’t know how to choose a server. Could anyone can tell me to process such a dataset, how…

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Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage?

Anyone know any clever snakemake/SLURM tricks to run a big analysis with limited storage? 1 I am using a SLURM HPC to run jobs and have ran into issues with storage. I have 3TB storage, and want to run over 1000 publicly available RNAseq data through my pipeline, which includes…

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how to align paired and unpaired fastq files of a sample using STAR?

how to align paired and unpaired fastq files of a sample using STAR? 2 Hi all I’m new to using STAR aligner. I have PE sequencing fastq files which have forward and reverse pairs and forward and reverse unpairs reads (4 files). In the manual of this tool, it seems…

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New bioinformatics method to analyze viral sgRNA

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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Valine tRNA levels and availability regulate complex I assembly in leukaemia

1. Rapino, F. et al. Codon-specific translation reprogramming promotes resistance to targeted therapy. Nature 558, 605–609 (2018). CAS  PubMed  Google Scholar  2. Goodarzi, H. et al. Modulated expression of specific tRNAs drives gene expression and cancer progression. Cell 165, 1416–1427 (2016). CAS  PubMed  PubMed Central  Google Scholar  3. Wolfe, A….

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ddPCR allows 16S rRNA gene amplicon sequencing of very small DNA amounts from low-biomass samples | BMC Microbiology

1. Lane DJ, Pace B, Olsen GJ, Stahl DA, Sogin ML, Pace NR. Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses. Proc Natl Acad Sci U S A. 1985;82(20):6955–9. PubMed  PubMed Central  CAS  Google Scholar  2. Vos M, Quince C, Pijl AS, de Hollander M, Kowalchuk GA. A…

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CMT2 Research Projects Launched by CMTA Seed Money Win NIH Funds

Two research projects focused on developing gene-editing therapies for Charcot-Marie-Tooth disease type 2 (CMT2) — both launched with seed monies from the Charcot-Marie-Tooth Association-Strategy to Accelerate Research (CMTA-STAR) program — have now been awarded additional funding from the National Institutes of Health (NIH). According to a CMTA press release, these NIH…

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STARsolo –EmptyDrops_CR parameters

STARsolo –EmptyDrops_CR parameters 1 I’m having some issues with the alignment of 10x scRNAseq data to a custom genome and I thought it would be good to do a stricter filtering on the cells so more cells get filtered out as empty droplets. Apparently STARsolo has several filtering algorithms, of…

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Blast command line pipeline not working

Blast command line pipeline not working 0 Hello, I am running now a local blast pipeline using MacOs. The goal here is to take interval of the 5 best hits and then extract the SNP variants from multiple vcf.gz files. But I am facing an error which I cannot solve….

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Indexing with STAR

Indexing with STAR 0 Hello, I am working with RNA seq data and creating an index of reference genome Gossypium hirsutum by using STAR. STAR asks GTF annotation format while my file is GFF3. According to literature, in order to run GFF file I need to remove –sjdbOverhang 50 and…

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Using STAR SJ.out.tab file to identify novel ncRNAs

Using STAR SJ.out.tab file to identify novel ncRNAs 0 Hi All, I am attempting to identify novel ncRNAs from a circadian RNAseq dataset. Specifically I have a ribo-depleted RNAseq timecourse with 31 samples (sample every 2 hours for 60hrs). I have run STAR (code below). I am trying to follow…

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Director of Bioinformatics Research Job Opening in Hudson, FL at M2GEN

Director of Bioinformatics Research Location:  Remote Status:  Full-time ExemptReports to:  VP Bioinformatics & BiostatisticsDirect Reports:  Build and lead a team consisting of bioinformatics research scientists that support internal business development client engagements, as well as, external academic partner research projects and biopharma sponsored bioinformatics services Who we are M2GEN is…

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The $11-billion Webb telescope aims to probe the early Universe

Lisa Dang wasn’t even born when astronomers started planning the most ambitious and complex space observatory ever built. Now, three decades later, NASA’s James Webb Space Telescope (JWST) is finally about to launch, and Dang has scored some of its first observing time — in a research area that didn’t…

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Containerization: Kubernetes 1.23 stabilizes operation with two network stacks

Kubernetes 1.23 is the third and final release of container orchestration this year. Among other things, it stabilizes the dual-stack operation in the cluster, the horizontal pod autoscaler and generic ephemeral volumes. With the new functions, initially introduced as alpha, the server-side validation of fields and the connection to OpenAPI…

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How is mitochondrial DNA (mtDNA) typing used in forensic science? a) A suspect’s mtDNA sample is

Suggest how coeliac disease could affect the growth of a child A solution has a pH of 2. Which best describes the solution? …answer: a strong acid What is the difference between a population and a community? Multiple choice question. cross out A) A population is made up of all…

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Create junctions from Bed file for IGV visualization

Create junctions from Bed file for IGV visualization 0 Any advice for creating junctions file from a bed-like file? My bed file looks like this: chr start end chr star end I have tried to copy the format used in TopHat (junctions file). But I can’t see the junctions in…

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Differentiation of hiPSCs Into Leydig-Like Cells

Takaki Ishida, Michiyo Koyanagi-Aoi, Daisuke Yamamiya, Atsushi Onishi, Katsuya Sato, Keiichiro Uehara, Masato Fujisawa, Takashi AoiEndocrinology, Volume 162, Issue 12, December 2021, bqab202doi.org/10.1210/endocr/bqab202 Abstract Late-onset hypogonadism (LOH) syndrome, due to a partial lack of testosterone, decreases the quality of life of older men. Testosterone is mainly secreted by Leydig cells…

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Index of /shares/gingeraslab/www-data/dobin/STAR/STARgenomes/Old/GENCODE/Old/GRCh38_Gencode21

Name Last modified Size Description Parent Directory   –   Genome 2014-11-25 11:42 3.0G   Log.out 2014-11-25 12:26 36K   SA 2014-11-25 12:13 23G   SAindex 2014-11-25 12:26 1.5G   chrLength.txt 2014-11-25 11:42 1.2K   chrName.txt 2014-11-25 11:42 3.2K   chrNameLength.txt 2014-11-25 11:42 4.4K   chrStart.txt 2014-11-25 11:42 2.1K  …

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featureCounts difference assigned reads summary file and summed up reads in feature count matrix

featureCounts difference assigned reads summary file and summed up reads in feature count matrix 0 Dear all, this might be a naive question but my googlefoo fails me. I count reads from a bam, aligend by Star against a custom hg19 genome, after running picard markDuplicates, then counting reads assigned…

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Analysts’ Top Conglomerates Picks: Deere (DE), Delta Airlines (DAL)

There’s so much to be optimistic about within the Conglomerates sector as 2 analysts simply weighed in on Deere (DE – Analysis Report) and Delta Airways (DAL – Analysis Report) with bullish sentiments. Deere (DE) Jefferies analyst Stephen Volkmann maintained a Purchase ranking on Deere yesterday and set a worth…

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Novartis (NVS) Highlights Growth Profile at its R&D Day

You’re reading Entrepreneur United States, an international franchise of Entrepreneur Media. This story originally appeared on Zacks Novartis NVS has provided a comprehensive view of its pipeline progress at its R&D Day held on Dec 2, 2021. – Zacks With a renewed focus on its core pharmaceutical business, the company…

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Bioinformatics Algorithms In Perl, Front end, Cedric Notredame 2001

Perl Implementation of some basic sequence comparison algorithms. PLEASE NOTE: These algorithms are only meant to be used as pedagogic support. They are simplified versions of the real stuff and are not meant to be used for research purposes. Program Description Usage hello_World.pl Hello World… hello_world bubble_sort.pl sorts number in…

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Error “start too small” when running htseq-count on a sorted .bam file

Error “start too small” when running htseq-count on a sorted .bam file 0 Hello, This is my first time aligning scRNA-seq reads to a reference genome to analyze differential gene expression. I am using htseq-count to obtain count files for my different samples and I am receiving the following error:…

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Getting errors trying to run rmats

Getting errors trying to run rmats 1 Hi, I am trying to use rmats for splice variation analysis through ssh using slurm after loading rmats module, these are commands that I tried and errors they produced rmats –s1 $PWD/control.txt –s2 $PWD/pdac.txt –gtf mm10/mm10.refGene.gtf Python programming language version 3.6.8 loaded. GNU…

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New bioinformatics method for viral sgRNA analysis

Single guide ribonucleic acid (sgRNA) molecules are produced by discontinuous transcription, in which viral RNA-dependant RNA polymerase pauses early negative-sense RNA synthesis and then jumps to the other end of the genome. The specifics of this process are still not fully understood. Since sgRNAs can play an important role in…

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Alexion Pharmaceuticals, Inc. hiring Bioinformatics Scientist in Boston, Massachusetts, United States

Some opportunities happen only once in a lifetime – like a job where you have the chance to change lives. At Alexion, people living with rare and devastating diseases are our Guiding Star. We are driven to continuously innovate and create meaningful value in all we do to help patients…

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Thinking Outside The Grid – A “bare bones” intro to Rtistry concepts in R using ggplot.

Recently I’ve discovered the courage to dive into creative coding and generative aRt in R. Something that the R community calls “Rtistry.” My Rtistry journey so far has been an amazing and tranquil expedition into a world that seemed intimidating and scary on the outside but is honestly just a…

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Error while aligning with STAR

Error while aligning with STAR 1 Hi, when I try to run this command. Note that I change working directory to directory containing fast files STAR –genomeDir /N/slate/ogaafer/mm10_index –runThreadN 8 –readFilesIn SRR8278856_1.fastq,SRR8278856_2.fastq SRR8278857_1.fastq,SRR8278857_2.fastq SRR8278859_1.fastq,SRR8278859_2.fastq –outSAMattrRGline ID:cont1 , ID:cont2 , ID:cont3 –outSAMtype BAM SortedByCoordinate –outSAMunmapped Within –outSAMattributes Standard I get this…

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How to calculate beta and SE from z-score , p-value and frequency

How to calculate beta and SE from z-score , p-value and frequency 0 Hi all, I have (an imputed) GWAS that only has z-score and p-values. I want to convert z-score into beta and SE. My ultimate goal is to use log(odds ratio) with its corresponding standard error to run…

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STAR index generation for bacterial genome

STAR index generation for bacterial genome 0 Hi, I’m trying to analyze RNA-Seq data for a bacteria – Mycobacterium tuberculosis. I used the FASTA and GTF files from NCBI to create the index, and set the –genomeSAindexNbases at 8 based on this previous post. The bash script I used is:…

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Alignment of de novo assembled transcripts to reference transcriptome?

Alignment of de novo assembled transcripts to reference transcriptome? 0 Hi all, I started with 40 samples of raw (but trimmed) RNASeq samples. I used these as inputs for SPAdes-rna and Trinity, to assemble them without a reference. I now have 80 assembled transcriptomes (?), and I tried to follow…

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STAR Genome indexing (Homo_sapiens_assembly38.fasta vs. GRCh38.primary_assembly.genome.fa)

I have a a query regarding STAR alignment. I used the following commands to generate genome index. (Homo_sapiens_assembly38.fasta) STAR –runMode genomeGenerate –genomeDir /home/bsh/BC_MCFcellLine_WTS/result/STAR_indexing/ –genomeFastaFiles /data1/database/ftp.broadinstitute.org/bundle/hg38_210610_download/Homo_sapiens_assembly38.fasta –sjdbGTFfile /home/bsh/BC_MCFcellLine_WTS/gencode.v27.annotation.gtf And I used the following commands for mapping and bam file was successfully generated. STAR –runThreadN 4 –outFilterType BySJout –outFilterMismatchNmax 999 –outFilterMultimapNmax 10…

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Collabera Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Job Description We have an exciting contract opportunity for a Bioinformatics Analyst to perform bulk differential gene. Ideally microarray and RNA-seq and enrichment analysis in the R programing language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene limma/variance Parition…

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UCL-BLIC/rnaseq – Giters

Introduction UCL-BLIC/rnaseq is a bioinformatics analysis pipeline used for RNA sequencing data, modified to add kallisto. The workflow processes raw data from FastQ inputs (FastQC, Trim Galore!), aligns the reads (STAR or HiSAT2), generates gene counts (featureCounts, StringTie) as well as kallisto abundance files, and performs extensive quality-control on the…

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pytorch implementation of openpose including Hand and Body Pose Estimation.

pytorch-openpose pytorch implementation of openpose including Body and Hand Pose Estimation, and the pytorch model is directly converted from openpose caffemodel by caffemodel2pytorch. You could implement face keypoint detection in the same way if you are interested in. Pay attention to that the face keypoint detector was trained using the…

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STAR alignment in a full directory

STAR alignment in a full directory 0 Hi! I’m working with STAR and I would like to align multiple file, but separately. I have file paires like these two: Dros_01_S48_L001_R1_001.fastq.gz Dros_01_S48_L001_R2_001.fastq.gz etc. Only the S[number] changes and the R1 and R2 in the names. I have a code, what I…

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Roche to present new data for its drug Polivy at the American Society of Hematology’s annual meeting

Roche will present a slew of new data at the American Society of Hematology’s (ASH) annual meeting next month, showcasing new immunotherapies, treatment combinations, novel endpoints and fixed-duration regimens from its blood disease portfolio. The company will present 90 abstracts, including 17 oral presentations. The new data, which includes results…

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Stacey Dash: Age, Wiki, Biography

Stacey Dash was born in the Bronx, New York. Stacy knew that she wanted to act, and from an early age began to act professionally. She made regular appearances on The Cosby Show (1984), The Fresh Prince of Bel-Air (1990), and also St. Elsewhere (1982). At 21 she made her…

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STAR alignment barely changes when limiting the maximum number of mismatches

STAR alignment barely changes when limiting the maximum number of mismatches 0 Hello everyone. I’m working with STAR aligner to map microRNA seq samples into the whole mouse genome. While taking a look at the parameters, I noticed the parameter —outFilterMismatchNmax had as default mismatch number 10 (according to the…

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FeatureCount summary in RNA_Seq analysis

FeatureCount summary in RNA_Seq analysis 0 Hi, I have a doubt about the number of reads mapped to genes in the featureCounts report. Is it possible that the number of reads mapped to genes is greater than the total number of reads? For exemple : Mapping repport : using STAR…

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I Won’t Disclose Vax Status Because I’ll Have to Share DNA Info Next

CNN Making some truly eyebrow-raising remarks about vaccines on Sunday, Virginia Lt. Gov.-elect Winsome Sears refused to share her vaccination status because she feels it is a “slippery slope” that will eventually lead to the disclosure of her DNA information. Sears, a rising Republican star who became both Virginia’s first…

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STAR for mouse RNA-seq alignment, which parameters should I use besides the basic ones in practice?

STAR for mouse RNA-seq alignment, which parameters should I use besides the basic ones in practice? 0 Hi Currently I have pair-end mouse RNA-seq data. 3 Tissues with 17 samples/tissue. Length of the sequence is from 100bp to 150bp. My goal is to perform DEG after the alignment. This is…

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STAR two -pass mode – lower alignment rate than one pass mode?

STAR two -pass mode – lower alignment rate than one pass mode? 0 Hi guys, Quick question. I’ve performed a two-step alignment with STAR 2.6a. It seems my unique alignment rates are approx 1% (85%) lower when performing two pass, than the original one pass mode (86%). I thought the…

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Weird output of geneCount for STAR?

Weird output of geneCount for STAR? 1 Hi I’m using STAR to perform alignment and my goal is to do the DEG analysis in the future. The parameter I set up as follows: Step 1: STAR –runThreadN 12 –runMode genomeGenerate –genomeDir genomedir –genomeFastaFiles ./ref/GRCm39.primary_assembly.genome.fa –sjdbGTFfile ./ref/gencode.vM27.primary_assembly.annotation.gtf –sjdbOverhang 100 Step 2:…

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Error after STAR mapping

Error after STAR mapping 0 Hi, I’m doing the STAR mapping, but I get the bam files with some problems.When I use the command samtools flagstat SRR7195620_2.fastq.gz_Aligned.sortedByCoord.out.bam to see the details of the bam file,it shows this: 3266075 + 0 in total (QC-passed reads + QC-failed reads) 1044500 + 0…

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Using STAR for mouse RNA-seq alignment, which parameters of STAR besides the basic ones would be better to use in practice?

Using STAR for mouse RNA-seq alignment, which parameters of STAR besides the basic ones would be better to use in practice? 0 Hi Currently I have pair-end mouse RNA-seq data. 3 Tissues with 17 samples/tissue. Length of the sequence is from 100bp to 150bp. My goal is to perform DEG…

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HPC-AI Advisory Council Announces the Winners of the 4th APAC HPC-AI Competition

36 Student Teams from Around the Asia Pacific (APAC) Region Participated in the Six-Month Long Competition which included Training and Hands-on Challenges SINGAPORE & SUNNYVALE, Calif., November 18, 2021–(BUSINESS WIRE)–The HPC-AI Advisory Council (HPCAIAC) and National Supercomputing Centre (NSCC) Singapore today announced the university team winners of its annual HPC-AI…

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Construction of circRNA-related ceRNA networks in longissimus dorsi muscle of Queshan Black and Large White pigs

Arcinas C, Tan W, Fang W, Desai TP, Teh DCS, Degirmenci U, Xu D, Foo R, Sun L (2019) Adipose circular RNAs exhibit dynamic regulation in obesity and functional role in adipogenesis. Nat Metab 1:16. doi.org/10.1038/s42255-019-0078-z CAS  Article  Google Scholar  Aronoff SL, Berkowitz K, Shreiner B, Want L (2004) Glucose…

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YOLOP | PyTorch

Before You Start To install YOLOP dependencies: pip install -qr github.com/hustvl/YOLOP/blob/main/requirements.txt # install dependencies YOLOP: You Only Look Once for Panoptic driving Perception Model Description   YOLOP is an efficient multi-task network that can jointly handle three crucial tasks in autonomous driving: object detection, drivable area segmentation and lane detection….

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Interploidy gene flow involving the sexual-asexual cycle facilitates the diversification of gynogenetic triploid Carassius fish

1. Muller, H. J. The relation of recombination to mutational advance. Mutat. Res. Mol. Mech. Mutagen. 1, 2–9 (1964). Google Scholar  2. Maynard Smith, J. The Evolution of Sex (Cambridge University Press, 1978). Google Scholar  3. Avise, J. C. Clonality (Oxford University Press, 2008). Google Scholar  4. Hamilton, W. D.,…

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very low mapping rate of polysome profling seq

very low mapping rate of polysome profling seq 0 when i use sequencing data from SRR7695423 frist, i use fastp to trim raw reads: fastp -i r1_fastq.gz -I r2_fastq.gz -o r1_trimmed_fastq.gz -O r2_trimmed_fastq.gz then i use STAR to align: STAR –runThreadN 20 –genomeDir index –readFilesIn r1_trimmed_fastq.gz r2_trimmed_fastq.gz –readFilesCommand ‘zcat’ –outFileNamePrefix…

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RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, which reference genome should I download when using STAR aligner?

RNA-Seq data for Lung, right ventricle (RV) and left ventricle (LV) of Mouse, which reference genome should I download when using STAR aligner? 1 I’m trying to perform alignment using STAR for my RNA-Seq data of Lung, right ventricle (RV) and left ventricle (LV) of Mouse, I wonder which reference…

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Image Recognition for Beginners using CNN in R Studio

Image Recognition for Beginners using CNN in R Studio Requirement Students will need to install R and RStudio software but we have a separate lecture to help you install the same Description You’re looking for a complete Convolutional Neural Network (CNN) course that teaches you everything you need to create an Image…

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Gene Ontology for the species Malus domestica

Gene Ontology for the species Malus domestica 1 Hi all, I mapped my reads using STAR and have feature counts. In R, I am using edgeR, limma, and voom for differential expression analysis. I did TREAT and glmMD plot. I have the differential expression list based on Gene-ID. For gene…

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3′ bias on polyA RNAseq goes wrong!

Hi! I’m checking the output from gene_bodyCoverage.py using a bed file with housekeeping genes. We sequenced some samples using a polyA capture library (all in the same kit, same sequencing run), so I would expect a 3′ bias. However, the output I got was somewhat mixed – I see some…

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“PyTorch Natural Language Processing Series” 9. NLP classics, frontiers and follow-ups

Translator | Liangchu In this chapter, we will review the previous chapters from the perspective of the entire book, see how the seemingly independent topics discussed in this book are interdependent, and understand how researchers can combine these content to solve the problem at hand. The problem. We will also…

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using rsem sample.genome.STAR.genome.bam for calculating expression

using rsem sample.genome.STAR.genome.bam for calculating expression 0 Hello, I have run rsem-calculate-expression on pair end sequencing. From the resulting BAM file mapped to the genome (sample.STAR.genome.bam), I would like to use that as in input to calculate expression of genes in the sample. When I try to use it as…

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Stable lariats bearing a snoRNA (slb-snoRNA) in eukaryotic cells: A level of regulation for guide RNAs

Significance Small nucleolar (sno)RNAs generally guide ribosomal RNA and small nuclear RNA modifications, essential events for ribosome and spliceosome biogenesis and function. Most are processed in the nucleus from lariat intronic RNAs, which are unstable byproducts of splicing. We report here that some snoRNAs are encoded within unusually stable lariats….

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Job Opening – Bioinformatics Analyst

job summary: As the world’s largest staffing and recruitment agency in the world, we can commit to find you the perfect role that gives you the opportunity to learn and grow in the life sciences arena. Utilizing a recruiter for your job search gives you access to a large network…

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STAR genomeSAindexNbases

STAR genomeSAindexNbases 0 Hello everyone! what is the exact meaning of the parameter genomeSAindexNbases which is used for building genome index by STAR? (the mannual says For small genomes, the parameter –genomeSAindexNbases must to be scaled down) Thanks a lot! Pei RNA-seq STAR mapping • 20 views • link 2…

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Review of popular science: analysis and comparison of single-cell RNA sequencing methods

Using 2i/LIF and ERCC inserted RNA cultured mouse embryonic stem cells (mESCs) as materials, using 6 different library preparation methods (CEL-seq2/C1, Drop-seq, MARS-seq, SCRB-seq, Smart-seq /C1 and Smart-seq2) prepare single-cell RNA-seq data. The difference between these methods lies in the use of unique molecular marker (UMI) sequences, which can distinguish…

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Synectics Inc. hiring Bioinformatics Analyst in North Chicago, Illinois, United States

Contract: 3 months Pay: $22.91/hr ONSITE Description Perform bulk differential gene (ideally microarray and RNA-seq) and enrichment analysis in the R programming language, leveraging public domain datasets from NCBI GEO/SRA and/or EBI ArrayExpress/ENA repositories. This includes performing quality control, normalization, differential gene (limma/varianceParition dream or other R method) and single-sample…

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