Tag: ATAC

identify and remove adapter sequence 2 Hi all, I am trying to identify the adapter sequences of my ATAC-sequencing data. The way I tried to achieve this was to send the fastq file to FastQC. Hoping the sequence would be picked and showed in the report. In the report, there…

NEW YORK – Droplet Genomics, a European technology company headquartered in Vilnius, Lithuania, is rolling out a new droplet microfluidic platform for high-throughput screening for a variety of research applications. CEO Juozas Nainys said the firm delivered the first of the instruments to customers at the end of 2021 after having…

Skin cutaneous melanoma (SKCM) is a type of highly invasive cancer originated from melanocytes. It is reported that aberrant alternative splicing (AS) plays an important role in the neoplasia and metastasis of many types of cancer. Therefore, we investigated whether ASEs of pre-RNA have such an influence on the prognosis…

Requisition # HRC0544032C Principal Investigator, Simon Knott, PhD is looking for a Postdoctoral Scientist to join the team! The Cedars-Sinai Center for Bioinformatics and Functional Genomics (CBFG) is an integrated, interdisciplinary research group with the common goal of developing end-to-end research workflows for genomic and high-throughput functional analysis of patient…

1. Li, H. et al. Classifying Drosophila olfactory projection neuron subtypes by single-cell RNA sequencing. Cell 171, 1206–1220 (2017). CAS  PubMed  PubMed Central  Google Scholar  2. Davie, K. et al. A single-cell transcriptome atlas of the aging Drosophila brain. Cell 174, 982–998 (2018). CAS  PubMed  PubMed Central  Google Scholar  3….

Details Posted: 23-Dec-21 Location: Evanston, Illinois Salary: Open Categories: Information Technology Staff/Administrative Department: MED-Center for Genetic MedSalary/Grade: EXS/8 Job Summary: Partners with clients to design, develop, implement and maintain business solutions regarding data management and analysis.  This includes database administration, data consolidation, data analysis and management reporting.  Utilizes software to…

Job Description A Research Fellow position is available in the Transcription and Chromatin Regulation Laboratory, School of Biological Sciences, Nanyang Technological University, Singapore. We are seeking a talented and motivated Research Fellow in computational biology or data analytics who is interested in developing machine learning approaches to study the changes…

Arrange the size of subplots in plotHeatmap deeptools figure 1 Hi all, I am trying to generate a 10×10 (10 bw files + 10 bed files) figure using deeptools but I am having trouble arranging the size of subfigures. I want the subfigures in the same size but if I…

Research Fellow (Computational Biology, Bioinformatics, Machine Learning) – Career at NTU University in Singapore. Apply for NTU University job and get your career at NTU University! Company: NTU University Job Type: Full Time Work Place: Singapore Salary: SGD 10000 / Month Job Description A Research Fellow position is available in…

All – Some years ago I was speaking to Sean Davis Re: the plethora of bioinformatics tools and databases. I commented to him that merely keeping up with what is available is difficult in the context of a full-time job, let alone mastering what you feel to be the best-in-class…

Hello, I am analyzing some ATAC-seq from flies using Diffbind3.0.8 and EdgeR. I initially ran dba.analyze() with the default peak size of 401 and was able to graph the results using dba.plotMA and dba.plotVolcano when my contrasts were evaluated using both EdgeR and DESEQ2. After resizing the peaks to 100…

Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from…

We are seeking multiple Experimental and Bioinformatics research positions (including Postdoctoral Research Fellows and Research Associate) to join the Alzheimer’s Network Medicine and Artificial Intelligence (AI) research group (www.lerner.ccf.org/gmi/cheng/) led by Dr. Feixiong Cheng at the Genomic Medicine Institute, Cleveland Clinic Lerner Research Institute, and Department of Molecular Medicine at…

tSNE and UMAP of scATAC-seq data looks like spaghetti 0 I would like to use R to generate cluster my 20k cells from a single cell ATAC-seq experiment. I ran PCA then selected the first 50 components, which were put into tSNE’s normalize_input() then Rtsne(). This is the result I…

DiffBind in Bioconda 1 @riba-michela-6472 Last seen 7 weeks ago Italy Hi, I was going to check my scripts for differential ATAC-seq Binding Analysis and wanted to install an updated version of “DiffBind” Bioconductor package, in particular version 3.2.6 or 3.2.4 in whcih a specific little bug that was present…

A Lead Bioinformatics Analyst position is available in the field of pharmacogenomics in the Savic laboratory. The primary research focus of the Savic laboratory involves studying the gene regulatory architecture of pediatric leukemia and genomic responses to antileukemic agents in order to define how the noncoding portion of the human genome impacts…

Med-Immunology – Pennsylvania-Pittsburgh – (21005833) Computational Immunogenomics Core is seeking a full-time data Bioinformatics Scientist. The candidate will be responsible for developing and deploying analytical workflows for multi-omics data from single-cell and ensemble genomics studies. The candidate will report to the core director and work with interdisciplinary teams to analyze…

How to merge samples of the same cell type to do differential peak calling? 1 Hi! Now I have 6 ATAC-seq samples which have been aligned to hg19 and called peaks by MACS2. 3 of them are from A cells and the other are from B cells. Now I’m going…

Benaroya Research Institute at Virginia Mason (BRI) has a bold mission: Predict, prevent, reverse and cure immune system diseases, from autoimmune disease to cancer to COVID-19. We examine the immune system in both health and disease to understand how disorders start and how to rebalance the immune system back to…

Position as Postdoctoral Research Fellow available at the Department of Biosciences. The appointment is a fulltime position and is made for a period of three years, and devoted to carrying out a project entitled URGE-3D, funded by the Norwegian Research Council. No one can be appointed for more than one…

We seek an outstanding and highly motivated early-career scientist in the fields of computational biology and/or bioinformatics. The position will involve novel integrated multimodal analyses of single cell datasets in blood immune cells and tissue. Qualified candidates will have an opportunity to design research projects that leverage cutting-edge approaches that…

The role: As part of the bioinformatics team, you’ll lead the development and prototyping of our flagship bioinformatics workflows (such as: RNAseq (single-cell, bulk, spatial), ChIP-Seq, ATAC-seq (single-cell and bulk), proteomics, etc.). For a given pipeline, you’ll research available analysis methods, compare and contrast existing bioinformatics tooling options, and define…

Cancer Sciences Location: Southampton General Hospital Salary: £31,406 Full Time Fixed Term (until 30/09/2022) Closing Date: Monday 06 December 2021 Reference: 1616921CM Applications are invited for a Post-doctoral Research Fellow to join the Cancer Genomics Research Group in the School of Cancer Sciences. This exciting Cancer Research UK-funded post aims…

About Benson HillBenson Hill empowers innovators to develop more healthy, tasty and sustainable food by unlocking the natural genetic diversity of plants. Benson Hill’s CropOS™ platform combines machine learning and big data with advanced breeding techniques and plant biology to drastically accelerate and simplify the product development process. The CropOS…

DOI: 10.18129/B9.bioc.epistack     This is the development version of epistack; for the stable release version, see epistack. Heatmaps of Stack Profiles from Epigenetic Signals Bioconductor version: Development (3.15) The epistack package main objective is the visualizations of stacks of genomic tracks (such as, but not restricted to, ChIP-seq, ATAC-seq,…

Seq2science is the attempt of the van heeringen lab to generate a collection of generic pipelines/workflows which can be used by complete beginners to bioinformatics and experienced bioinformaticians alike. Please take a look at our docs for help with installation, how to run it, and best practices. Our supported workflows:…

How to define open or close gene in ATAC-seq? 0 May I ask how do you use your ATAC-seq data for post-alignment analysis? Here’s what I’m doing and I have a few problems: For example, there are two groups of samples, WT and KO. In order to define the peak…

1. Wu, S. et al. Circular ecDNA promotes accessible chromatin and high oncogene expression. Nature 575, 699–703 (2019). 2. Gorkin, D. U., Leung, D. & Ren, B. The 3D genome in transcriptional regulation and pluripotency. Cell Stem Cell 14, 762–775 (2014). CAS  PubMed  PubMed Central  Google Scholar  3. Zheng, H….

The Biostar Herald publishes user submitted links of bioinformatics relevance. It aims to provide a summary of interesting and relevant information you may have missed. You too can submit links here. This edition of the Herald was brought to you by contribution from Mensur Dlakic, Istvan Albert, and was edited…

Overview At the heart of QIAGEN’s business is a vision to make improvements in life possible. We are on an exciting mission to make a real difference in science and healthcare. We are still the entrepreneurial company we started out as and have today achieved a size where we can…

Retinoic acid affects the transcriptome of zebrafish endodermal cells To identify genes regulated by RA in zebrafish endodermal cells, we used the transgenic Tg(sox17:GFP) line which drives GFP expression in endodermal cells and allows their selection by fluorescence activated cell sorting (FACS). Tg(sox17:GFP) embryos were treated either with RA, BMS493…

Summary We are looking for a talented and motivated individual to work with teams of Researchers and Scientists providing bioinformatics training, consulting, application development and support as part of the Center for Advanced Genomic Technologies (CAGT). Work performed • Contribute to the design, development, implementation, and testing of bioinformatic tools…

DepartmentBSD PED – Section Administrator: Hematology, Oncology, and Stem Cell Transplantation About The Department The Section of Pediatric Hematology/Oncology provides care for patients and families with acute and chronic medical conditions, or other hematologic diseases, requiring the specialty knowledge and skills of Hematology, Oncology and Stem Cell Transplantation. Job Summary…

On November 9, 2021, the Stem Cell and Regenerative Medicine Center of the Department of Basic Medicine, Zhejiang University School of Medicine/The First Affiliated Hospital of Zhejiang University School of Medicine/Zhejiang Liangzhu Laboratory Zhang Jin’s research group published a titled ” rRNA Biogenesis ” in Nature Communications . Regulates Mouse…

1. Chapman, N. M., Boothby, M. R. & Chi, H. Metabolic coordination of T cell quiescence and activation. Nat. Rev. Immunol. 20, 55–70 (2020). CAS  PubMed  Google Scholar  2. Kim, J. & Guan, K. L. mTOR as a central hub of nutrient signalling and cell growth. Nat. Cell Biol. 21,…

Can I directly use MACS2 -t -c for ATACseq differential analysis on WT and KO sample? 0 I have ATACseq data from one WT sample and one KO sample, and want to find different peaks between them. Can I just use MACS2 -t -c for this purpose? For example, MACS2…

Parexel International Corporation USA – Any Region – Home Based The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for…

100% Postdoctoral Position in Bioinformatics to study Gene Regulatory Networks 2-2.5 year fixed-term contract available immediately or as agreed Understanding how a fertilized egg develops into a complex multicellular organism is one of the most fascinating topics in biology. The current challenge is to understand how genes function as part…

The Senior Scientist operationally delivers client projects for Biomarker and Genomic Medicine (BGM) services. S/he demonstrates deep knowledge of scientific principles and concepts related to one or more capabilities and is experienced in industry standards. S/he will provide support for the BGM strategy and interpretation to other SBUs and clients….

Significance In this study, we show that the inactivation of the gli3 gene in medaka fish results in the formation of larger dorsal and paired fins. These mutant fins display multiple radial bones and fin rays which resemble polydactyly in Gli3-deficient mice. Our molecular and genetic analyses indicate that the…

Do you remove blacklisted regions before or after calling peaks? 0 Hello, I have a question about ATAC-seq processing. I’m working with mouse data where blacklisted regions typically get removed during processing. Some tutorials remove blacklisted regions from the BAM file before calling peaks. Others do this step afterwards on…

TSS enrichement plot : Are scores different between paired and single end ? 0 I’m using this script from ATAqc to compute my TSS enrichment score for ATAC-seq data. But my values are pretty high, around 20+. I was wondering if this script, using the metaseq package was not counting…

7219 07-11-2021 May 23,  · Although tools like FASTQC presents a graph showing sequence duplication levels understanding and interpreting duplication is complicated for many users by the fact they are working with single-end sequence data, e.g. most RNA-seq or ChIP-seq datasets. In the worst…

Attend this webinar to learn how to win a NextSeq 2000 P3 200-cycle flow cell for your lab – that’s A BILLION READS of sequencing for FREE. See terms and conditions.  Innovations in next-generation sequencing are helping the UMN genomics community ask – and answer – increasingly complex scientific questions. …

With over 35 nationalities and a range of backgrounds represented in our Benevolent team, we aim to build an inclusive environment where our people can bring their authentic selves to work, be respected for who they are and the exceptional work they do. We welcome and actively encourage applications from…

How to interpret Nucleosome banding pattern in scATAC-Seq? 0 Hello, I am following Signac vignette to perform QC on my single cell ATAC-Seq data. As per my understanding the vignette considers all cells with nucleosome signal > 4 to have a high nucleosomal signal strength and nucleosome signal is calculated…

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…

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

Junior Bioinformatician at the Lymphoma Genomic Laboratory Open position Junior Bioinformatician at the Lymphoma Genomic Laboratory Institute of Oncology Research (IOR) Bellinzona, Switzerland www.ior.usi.ch www.ior.usi.ch The Institute of Oncology Research (IOR) in Bellinzona, Switzerland, is a rapidly evolving,leading center for basic and translational research in oncology in Europe.IOR is affiliated…

Position Title Bioinformatics Associate I/II Classification: Exempt Who is Active Motif? Active Motif, Inc. is a privately held global biotechnology company with the vision of bringing the field of epigenetics into personalized and precision medicine. Active Motif’s Bioinformatics group performs specialized transcriptomic- and epigenetics-based analyses for leading academic groups and…

Measure genome-wide agreement of peaks in 0 Is there an approach to measure agreement in epigenomic signals e.g. histone marks (continuous -log10 p-vals after peak calling)? This approach should also work across assays or cell types. For example, how similar is the DNAse-seq signal across Neutrophils, Monocytes and T-cells? Are…

Scientist II, Cancer Immunologic Data Commons Dana-Farber Cancer Institute Boston, MA Full Time PTL Remote: 2-3 days remote/wk The Department of Data Science seeks a Scientist II to lead the development of the Cancer Immunologic Data Commons at Dana-Farber. The Scientist II will work closely with the laboratories of Drs.Franziska…

My ATAC-seq data returns a peak of 1bp for all the peak intervals when using DiffBind’s dba.count(summit=0). why is this happening? 0 The binding matrix’s peak intervals (all of them) have a width =1 bp. I have set summit=False, summit=0, summit=True. All these parameters return 1 bp width. In fact,…

Running ATAC-Seq pipeline from ENCODE 1 SLURM is simply a scheduler on HPC systems. You can (probably) just save the script and run it as bash that_script.sh. Alternatively, consider the nf-core ATAC-seq pipeline: nf-co.re/atacseq Login before adding your answer. Traffic: 1212 users visited in the last hour Read more here:…

why are all DiffBind tutorial’s ATAC-seq peak intervals 400 bp for all intervals? 1 I have followed DiffBind tutorial bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf I have found out that the returned count matrix’s peak intervals are always 400bp. Literally, all the peak intervals in the count matrix are 400 bp. I am wondering why…

Surrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway.Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from Stanford…

As a Staff Bioinformatic Research Engineer and Senior Manager at Freenome, you will lead a team responsible for developing and deploying bioinformatics research on Freenome’s ML research platform. You will lead and manage a team of Research Engineers working large multi-omic datasets, including whole-genome sequencing of cell-free DNA, extracellular small…

How to import a BED file to ChIPseeker in order to visualize genome coverage plot? 1 Could you please explain how to connect the ATAC-Seq peak results discovered by DiffBind to be imported to ChIPseeker to get CHIP peaks coverage plot? For example, I have the following bed file. chr14…

A postdoctoral position (3 years with possible extensions) is available immediately in the evolutionary genomics group of Henrik Kaessmann. We are seeking highly qualified and enthusiastic applicants with strong skills in computational biology/bioinformatics, ideally also with experience in data mining and comparative or evolutionary genome analyses. We have been interested…

Confused by MACS2 –scale-to option 1 Hi all, Quick Q regarding MACS2. The manual states that the –scale-to option serves to “scale the larger sample up to the smaller sample” or vice-versa. What exactly does it mean by this? Is this scaling only applied when multiple samples/reps are given? Or…

DOI: 10.18129/B9.bioc.esATAC     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see esATAC. An Easy-to-use Systematic pipeline for ATACseq data analysis Bioconductor version: 3.12 This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw…

DescriptionSurrozen is a biotechnology company focused on discovering and developing novel regenerative medicines that unlock the powerful self-renewal properties of the body through specific control of the Wnt signaling pathway. Surrozen was founded by five leading-edge scientists: K. Christopher Garcia, Ph.D., Roel Nusse, Ph.D. and Calvin Kuo, M.D., Ph.D. from…

Position Description: Every great life-changing discovery begins the same way—with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do at the Medical College of Wisconsin….

using DESeq2 for ATAC analyses 1 @changxufan-24128 Last seen 23 hours ago United States I love DESeq2! However, when using DESeq2 for ATAC analysis, I realized one potential issue. In the figure below: Left is a scatter plot between 2 samples (biological replicates). Each point represents the read count at…

How can I export raw count profile from DiffBind to be analyzed on DESeq2 separately? 0 I am performing some ATAC-seq analysis. I would like to export the output files as a raw abundance profile so that I can analyze them on DESeq2 separately. I am aware that DiffBind contains…

Employer Name: Albert Einstein College of Medicine Specific Responsibilities: Processing and mapping raw NGS RNA-seq, ChIP-seq, ATAC-seq, WGBS and other omics datasets. Analyzing RNA-seq, ChIP-seq, ATAC-seq, WGBS and other omics data sets generated in the lab for investigation of gene and chromatin regulatory networks in stem cells and cancer. Downloading…

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

How to select a few TF binding site using JASPAR on UCSC 1 I’m trying to find Transcription factor binding sites using JASPAR on UCSC. The area of thee genome I am interested in ends up having a lot of TF binding site, is there a way to customize JASPAR…

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…

Job Description Diagenode (a Hologic company) is an international biotech company that develops and commercializes innovative instruments and reagents systems for the life science research and molecular diagnostics. Founded in 2003, the Group is headquartered in Liège (Belgium), with subsidiaries in Denville (NJ, USA), in Toyama (Japan) and in Santiago…

Bioinformatics Research Scientist – 93904 Organization: JG-Joint Genome Institute Lawrence Berkeley National Lab’s (LBNL, www.lbl.gov/) Joint Genome Institute Division (jgi.doe.gov/) has an opening for a Bioinformatics Research Scientist to join the team. In this exciting role, you will develop new computational methods to investigate gene regulation and regulatory sequence properties…

(Level A) $89,610 to $96,007 per annum and (Level B) $100,933 to $119,391 per annum plus an employer contribution of up to 17% superannuation may apply Two fixed-term, full-time positions available for three years Two exciting Bioinformatic opportunities in the newly established Adelaide Centre for Epigenetics (ACE) These two positions…

The Dorrity group at EMBL Heidelberg is seeking a highly motivated computational biologist to act as a Laboratory Officer, helping to set up a new lab that promotes a welcoming and positive atmosphere. Our group uses single-cell genomics as a whole-organism phenotyping tool in zebrafish to (1) understand how different…

How to use MACS2 output for DESEQ2 differential analysis during ATAC-seq? How to get the intersect? 0 I have processed my ATAC-seq reads and finally obtained MACs2 output bed files. I am at a loss to proceed from here to DESeq2 analysis. I will be thankful to you if could…

Job Description Bioinformatics Scientist Med-Immunology – Pennsylvania-Pittsburgh – (21005833) Computational Immunogenomics Core is seeking a full-time data Bioinformatics Scientist. The candidate will be responsible for developing and deploying analytical workflows for multi-omics data from single-cell and ensemble genomics studies. The candidate will report to the core director and work with…

SummaryAn open position for a Bioninformatic Analyst I is available in the Department of Ophthalmology, Baylor College of Medicine, Houston, TX. Will work alongside research scientists and clinicians with diverse backgrounds, including other bioinformaticians and computational biologists, molecular biologists, geneticist and immunologists. The work will focus on harnessing the power…

Job ID: 1080691_RR00048323 NYU Grossman School of Medicine is one of the nation’s top-ranked medical schools. For 175 years, NYU Grossman School of Medicine has trained thousands of physicians and scientists who have helped to shape the course of medical history and enrich the lives of countless people. An integral…

What you describe seems to be a difference in signal-to-noise ratio which is not uncommon. This is where more elaborate normalization methods such as TMM from edgeR or RLE from DESeq2 come into play. See the following links on why these methods are superior. The videos talk about RNA-seq but…

Forum:Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols 2 Published in the RNA Journal in 2020 – this paper argues that if the original RNA amount in the different samples is different, TPM should not be used to find differentially expressed genes. www.ncbi.nlm.nih.gov/pmc/articles/PMC7373998/ Seems like…

Hi people, Currently, I’m working on analyzing ATACseq data with the following pipeline: fastQC, adapter trimming, etc. BWA mem Remove duplicates, filter MAPQ Call peaks with Genrich for all samples Merge all sample peaks into reference peak set Count Tn5 cut sites with featureCounts At this point I have a…

Today, we can produce more biomedical data in about three months than we did in the past, with petabytes from just a single hospital. There is a deluge from various sources, such as patients’ medical records, medical instruments, lab work, and more. Likewise, in the research and development space, similar…

We are extending our bioinformatics team and are seeking for two enthusiastic bioinformaticians who would like to build and advance their career in translational cancer genomics and/or spearhead the implementation of next generation sequencing methodologies in routine cancer diagnostics and precision medicine. As a bioinformatician, you will conduct analyses of…

Is there any software that can use ATAC-seq to identify super enhancer 1 Hello Everyone! Has anyone tried to identify super-enhancers by using ATAC-seq? I am wondering whether some one can recommend some software 🙂 Thanks a lot in advance for your comments and ideas! Best wishes Guandong Shang ATAC-seq…

EPFL, the Swiss Federal Institute of Technology in Lausanne, is one of the most dynamic university campuses in Europe and ranks among the top 20 universities worldwide. The EPFL employs more than 6,000 people supporting the three main missions of the institutions: education, research and innovation. The EPFL campus offers…

Bioinformatics and Biostatistics Core Facility   Reports to: Head of Bioinformatics Core Facility   This is a full-time, permanent position on Crick Terms and Conditions of Employment.                                              …

Short summary The position of Bioinformatics Training Developer will provide support to the bioinformatics training and development needs of research scientists primarily RNA-Seq, ATAC-Seq, ChiP-Seq and single-cell RNA-Seq. There are 2000 research scientists at the Francis Crick Institute. The role-holder will be located within the Bioinformatics and Biostatistics Core in…

Hi. I’m doing ATAC-seq analysis of colon tissue. I analyzed 1)QC -> 2)Mapping -> 3)Post alignment processing(remove mt reads, duplicated reads, multi-mapped reads) -> 4)Peak calling order. However, as a result of calculating FRiP after peak calling using MACS2, the FRiP score was too low. No major problems were found…

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)…

Description Overview We are looking for a highly motivated and creative bioinformatics research scientist to develop and apply innovative analytical approaches to understand the genetic modifications that drive the development and response to therapy of blood tissues. The scientist will contribute ideas to implement automate and improve existing analysis methods,…

Calling differential peaks on ATAC-seq data 0 My lab has recently run an ATAC-seq analysis on 3 biological conditions (Day 0, day 1 and day 7) with two replicates assigned to each. Once the data is finally generated, I will need to use some differential peak calling software to identify…

Manager, Bioinformatics Brain Science The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make…

Feature selection 0 Hello, I am starting out with bulk ATAC data as bed files that include the read counts. I want to use this data for a package called MOFA, which requires these preprocessing steps: Normalisation: For count-based data such as RNA-seq or ATAC-seq we recommend size factor normalisation…

edgeR parameters 0 I have a doubt regarding filtering results of edgeR I am not getting how to consider whether our genes which we got from edgeR are significant or not.We got 22,000 genes but I need to filter .The parameters set wereMin CPM =1, Log2fc=0,Pvalue adj=0.05. How should I…

Dear all, I am trying to follow the WNN vignette here satijalab.org/seurat/articles/weighted_nearest_neighbor_analysis.html After the steps below, I would like to annotate my clusters, hence I need to know the markers which best represent each cluster. pbmc <- FindMultiModalNeighbors(pbmc, reduction.list = list(“pca”, “lsi”), dims.list = list(1:50, 2:50)) pbmc <- RunUMAP(pbmc, nn.name…

How to get Read Counts from MACS2 output files? 0 Hello, I am working with GEO datasets that supply both bigwig(bw) and bed files for each ATAC sample. I need the read counts/pile up value for downstream analysis, but the 6+4 narrow peak file format from MACS2 does not include…

Species invasions into novel habitats mark major transitions in the evolution of life on Earth. Some of these are relatively ancient, such as the vertebrate transition from the oceans to life on land (∼375 Mya) or the evolution of arboreal vertebrate species (∼160 Mya). When divergent lineages transition to the…

Normalization and differential analysis in ATAC-seq data 2 Hello everyone! I would like to know if someone had experiences with normalization and differential expression on ATAC-seq data. After using MACS2 for the peak calling, how can we use Dseq2 or EdgeR on these datas? Someone try this? What is the…

Prostate cancer is the most common male cancer and approximately 5,000 Finnish men are diagnosed with it each year. While most prostate cancers are not aggressive, some tumors develop into a deadly castration-resistant form of the disease. One of the most significant clinical challenges today is deciding which type of…

CTCF is a transcription factor that has been a research target due to its role in regulating a critical oncogene called MYC. Scientists at St. Jude Children’s Research Hospital have found direct evidence that CTCF governs chromatin accessibility, the process of opening tightly spooled DNA so that genes can be…

Position Description: Every great life-changing discovery begins the same way-with new knowledge. It can change everything, from a single life to the future of entire communities. That’s why academic medicine, and the continuous pursuit of knowledge, is at the center of everything we do…