Tag: MACS

What Is The Meaning Of The Score In Diffbind’S Occupancy/Overlap Analysis?

I have 3 chip-seq biological replicates, each with its own input control. I was interested in using diffBind to performs some IDR-style analysis – e.g. take only the peaks that come up in more than one sample. experiment <- dba(sampleSheet=”exp_samples.csv”) pdf(‘overlap_venn.pdf’) dba.plotVenn(experiment, experiment$masks$macs) dev.off() I got a nice Venn diagram:…

Continue Reading What Is The Meaning Of The Score In Diffbind’S Occupancy/Overlap Analysis?

Single-cell analysis of chromatin accessibility in the adult mouse brain

Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…

Continue Reading Single-cell analysis of chromatin accessibility in the adult mouse brain

Overlapping and merging ChIP-seq peaks

Overlapping and merging ChIP-seq peaks 0 Hi all, I have ChIP-seq data sets for two different proteins (let’s call them A and B) in the same cell line that need to form a dimer in order to function as an active TF. Protein A can form either a homodimer (A/A)…

Continue Reading Overlapping and merging ChIP-seq peaks

Origin and evolution of the triploid cultivated banana genome

Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS  PubMed  PubMed Central  Google Scholar  Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…

Continue Reading Origin and evolution of the triploid cultivated banana genome

Will RStudio ever been available on the Mac App Store? – RStudio IDE

Continuing the discussion from Is an iPad version of RStudio under development? Will RStudio ever be available on the Mac App Store?: I was on Mastodon bemoaning the fact that I found yet another student using RStudio from within the virtual install ‘disk’ that gets mounted on Macs during installation,…

Continue Reading Will RStudio ever been available on the Mac App Store? – RStudio IDE

Apple launches MLX machine-learning framework for Apple Silicon

Apple’s machine learning (ML) teams have released a new ML framework for Apple Silicon: MLX, or ML Explore arrives after being tested over the summer and is now  available through GitHub. Machine Learning for Apple Silicon In an X-note, Awni Hannun, of Apple’s ML team, calls the software: “…an efficient machine…

Continue Reading Apple launches MLX machine-learning framework for Apple Silicon

How is “integer score for display” calculated in MACS2

How is “integer score for display” calculated in MACS2 2 Hi all, In the MACS2 output file “NAME_peaks.narrowPeak”, there’s a column called “integer score for display”. I found the score is not proportional to the 7th column “fold-change”. For example, I have two peaks. The “integer score for display” and…

Continue Reading How is “integer score for display” calculated in MACS2

Genetic risk converges on regulatory networks mediating early type 2 diabetes

Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

Continue Reading Genetic risk converges on regulatory networks mediating early type 2 diabetes

Chipseq peak calling and peak frequency region

I am working on Chip seq data, I have implemented the chipseq pipeline with spike in method and called peaks using MACS2. The same data has been analyzed before in my lab, and my peaks show a similar pattern as the previous ones . By this I meant that the…

Continue Reading Chipseq peak calling and peak frequency region

Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification

Introduction The development of multicellular organisms requires the activation of different gene batteries which specify the identity of each individual cell type. Such shifts in cellular identity are driven by shifts in the gene regulatory network (GRN) consisting of transcription factors (TFs) binding to the enhancers and promoters of their…

Continue Reading Chromatin priming elements direct tissue-specific gene activity before hematopoietic specification

Use of IDR after running MACS3 for ATAC-seq data

Use of IDR after running MACS3 for ATAC-seq data 0 Cross-posted from github (a little worried about the inactivity there; please let me know if this is not good practice) I am analyzing ATAC-seq data from human cells. I am planning to perform the following as part of my pipeline:…

Continue Reading Use of IDR after running MACS3 for ATAC-seq data

MD Anderson Research Highlights for November 15, 2023

Newswise — HOUSTON ― The University of Texas MD Anderson Cancer Center’s Research Highlights showcases the latest breakthroughs in cancer care, research and prevention. These advances are made possible through seamless collaboration between MD Anderson’s world-leading clinicians and scientists, bringing discoveries from the lab to the clinic and back. Recent…

Continue Reading MD Anderson Research Highlights for November 15, 2023

frequency plot for peaks

Hello, I am computer science student and trying to work on BioMedical data and learning and applying the Bioinformatics techniques. I have ChipSEQ data generated by my lab , of histone modification , H3k27me3, with three different samples I have applied the whole pipeline and able to call peaks as…

Continue Reading frequency plot for peaks

bedgraph-to-bigwig error – usegalaxy.eu support

Adrian1 November 12, 2023, 10:30pm 1 tool: bedgraph-to-bigwig input: bedgraph files from MACS2 output problem: result bigwig file has 0 lines tool standard output: hashMustFindVal: ‘GL456210.1’ not foundtool standard error” grep: write error: Broken pipe Error running wigToBigWig. more details: I used mm39 as the database/build for all my inputs,…

Continue Reading bedgraph-to-bigwig error – usegalaxy.eu support

argument is of length zero

Hi Diffbind community! I have been encountering some errors creating dba object because the Diffbind package can not load the files. I tried using the aligned bam files after creating sample sheet but have been getting following error: “Error in if ((length(callers) == 1) & (callers[1] == “counts”)) { :…

Continue Reading argument is of length zero

TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Padeken, J., Methot, S. P. & Gasser, S. M. Establishment of H3K9-methylated heterochromatin and its functions in tissue differentiation and maintenance. Nat. Rev. Mol. Cell Biol. 23, 623–640 (2022). Article  CAS  PubMed  PubMed Central  Google Scholar  Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation…

Continue Reading TNRC18 engages H3K9me3 to mediate silencing of endogenous retrotransposons

Highly oxidized albumin is cleared by liver sinusoidal endothelial cells via the receptors stabilin-1 and -2

List of reagents Chloramine-T trihydrate (Merck, Darmstadt, Germany), Copper(II)Sulphate, Penicillin, Streptomycin, RPMI-1640 (Sigma-Aldrich, Burlington, MA, USA), RPMI-1640 (Euroclone, Pero, Italy), DMEM low glucose (Sigma-Aldrich), Trypsin–EDTA (Sigma-Aldrich), Blasticidin hydrochloride (Sigma-Aldrich), Trichloroacetic acid (Merck), Fetal Bovine Serum (Merck, Darmstadt, Germany), Iodine 125 Radionuclide (Perkin Elmer, Waltham, Mass., USA), Iodogen™ iodination reagent (Pierce,…

Continue Reading Highly oxidized albumin is cleared by liver sinusoidal endothelial cells via the receptors stabilin-1 and -2

Single-cell transcriptomics reveals the brain evolution of web-building spiders

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

Continue Reading Single-cell transcriptomics reveals the brain evolution of web-building spiders

Fasting-Mimicking Diet Drives Antitumor Immunity against Colorectal Cancer by Reducing IgA-Producing Cells | Cancer Research

Fasting-mimicking diet (FMD) is emerging as an effective dietary intervention with the potential to prolong life span in healthy people and boost antitumor immunity in patients with cancer. FMD refers to a medically designed fasting-like state that allows periodic consumption of a very-low-calorie and low-protein diet (1, 2). Compared with…

Continue Reading Fasting-Mimicking Diet Drives Antitumor Immunity against Colorectal Cancer by Reducing IgA-Producing Cells | Cancer Research

How to give the defined p value in MACS2 command line (peak calling)

How to give the defined p value in MACS2 command line (peak calling) 1 I am using this command line for peak calling but it automatically sets the p-value to 0 .05 I want to change it to 0.01. Please suggest where I have to set it to 0.01 Please…

Continue Reading How to give the defined p value in MACS2 command line (peak calling)

Apple announces new 14-inch and 16-inch MacBook Pros with M3 chips

Today at the Scary Fast event, Apple announced updated 14-inch and 16-inch MacBook Pros with new M3 chips. These new chips deliver remarkable performance improvements over the previous M1 and M1 Pro/Max chips. The entry-level 14-inch MacBook Pro now features the M3 chip. Apple says it is up to 60%…

Continue Reading Apple announces new 14-inch and 16-inch MacBook Pros with M3 chips

Sequence Submission to Gen Bank – SEQUENCE SUBMISSION TO GENBANK The GenBank DNA sequence database

SEQUENCE SUBMISSION TO GENBANK The GenBank DNA sequence database is an international collection of all known DNA sequences. GenBank is produced and distributed by the National Center for Biotechnology Information (NCBI), a division of the National Library of Medicine at National Institute of Health (NIH). One of the most important…

Continue Reading Sequence Submission to Gen Bank – SEQUENCE SUBMISSION TO GENBANK The GenBank DNA sequence database

MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Introduction After the fusion of the oocyte and sperm, the zygote undergoes a series of cell divisions until it forms a blastocyst before implantation into the uterus. A human blastocyst is formed of a fluid-filled cavity and ∼200 cells that comprise three distinct cell types: the trophectoderm (TE), which gives…

Continue Reading MICA: a multi-omics method to predict gene regulatory networks in early human embryos

Get the strongest TF binding regions for Chip-Seq

Get the strongest TF binding regions for Chip-Seq 0 Hi All, Is there a package / program that finds the peaks with the most differential pileup between the condition and input? For example, I am currently calling peaks with HOMER and MACS2; these programs automatically determine if the amount of…

Continue Reading Get the strongest TF binding regions for Chip-Seq

Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice

Mouse strains All mouse procedures were approved by the Institutional Animal Care and Use Committees at Binghamton or Stanford University; and were conducted in accordance with the National Institute of Health Guide for Care and Use of Laboratory Animals, Eighth Edition. All mice were originally obtained from Jackson Laboratories, and…

Continue Reading Neuron Navigator 1 (Nav1) regulates the response to cocaine in mice

macs2 output r file not generated

macs2 output r file not generated 1 Hello I am working on chipseq data, for peak calling I used macs2 and following command. As an output its generating the bdg file but no R file is being generated Kindly suggest what am I doing wrong. macs2 callpeak \ -t _unique_rmdup_sampled.bam…

Continue Reading macs2 output r file not generated

anish-shanbhag’s Profile | Apple Developer Forums

Post not yet marked as solved Is there any way to train PyTorch models directly on-device on an iPhone via the GPU? PyTorch Mobile docs seems to be completely focused on inference only, as do the iOS app examples (github.com/pytorch/ios-demo-app). I did find this article about using MPS backend on…

Continue Reading anish-shanbhag’s Profile | Apple Developer Forums

ChIPseq gapped and braod peaks file are empty

ChIPseq gapped and braod peaks file are empty 0 Hello, I am using macs2 for peak calling , on ChIPseq data using the following command. I have done the normalization using the drosophila genome on my data. macs2 callpeak -t /Normalized_samples_ip/_IP_unique_rmdup_sampled.bam \ -c _001_unique_rmdup_sampled.bam -f BAM –gsize 3.0e9 –broad –broad-cutoff…

Continue Reading ChIPseq gapped and braod peaks file are empty

MACS3 installation

MACS3 installation 1 I am trying to install MACS2/MACS3 in the Ubuntu 20.04 environment. I am having issues I have no idea how to solve (fairly new to this environment and this is my first post!). Using the commands: sudo apt install MACS3 or pip install MACS3 (and for MACS2…

Continue Reading MACS3 installation

Genome-wide chromatin interaction map for Trypanosoma cruzi

Johnson, P. J., Kooter, J. M. & Borst, P. Inactivation of transcription by UV irradiation of T. brucei provides evidence for a multicistronic transcription unit including a VSG gene. Cell 51, 273–281 (1987). Article  CAS  PubMed  Google Scholar  Matthews, K. R., Tschudi, C. & Ullu, E. A common pyrimidine-rich motif…

Continue Reading Genome-wide chromatin interaction map for Trypanosoma cruzi

ggplot2 – Heatmap style ggplot showing values using color in R

I am trying to create a plot like the following: That is, a plot which has darker color based on the value (with white representing 0) in ggplot. I have some dataframe library(tidyverse) library(ggplot2) macs <- c(1,2,3,4,5,6) KP <- c(4,5,0,7,8,2) PF <- c(4,6,8,0,3,1) df <- data.frame(macs,KP,PF) rownames(df) <- c(“PelTrawl”,”DemTrawl”,”KelpHarv”,”DemSeine”,”Rifles”,”Nets”) That…

Continue Reading ggplot2 – Heatmap style ggplot showing values using color in R

Design model includes sex but only one female

I have a question about how DESeq2 handles design models which include a parameter that only applies to a single sample in the dataset. For context, we are using DESeq2 to capture differential chromatin accessibility due to age differences (adult vs juvenile) using CUT&RUN data from the venom glands of…

Continue Reading Design model includes sex but only one female

Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening

Construct design To transcribe and translate sequenced DNA clusters on an Illumina flow cell, our DNA constructs contained the following elements: a P5 adaptor, followed by a 28 nt unique barcode, a 27 nt unstructured spacer (5p UNS v2), a ribosome binding site, start codon, protein coding region, TolAk short linker, 2×…

Continue Reading Rapid discovery of high-affinity antibodies via massively parallel sequencing, ribosome display and affinity screening

Summit Extension in Cut&tag analysis

Summit Extension in Cut&tag analysis 0 I am doing a cut-tag analysis to find the motif of a protein(a transcription factor),and i have got narrowPeak file and summit file from macs2,and now i want to find motif via meme-chip,the question is: should i use extended sequences from summits for motif…

Continue Reading Summit Extension in Cut&tag analysis

DiffBind dba.count() crash/can’t finish problems

I am using Diffbind for an ATAC-Seq analysis. My peak caller is MACS2, and here is my sample sheet: I run Diffbind with the following codes, but it crashed every time on dba.count . it can finished Computing summits… Recentering peaks… Reads will be counted as Paired-end. But have this…

Continue Reading DiffBind dba.count() crash/can’t finish problems

Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?

MacOS M1 is probably the best system you could purchase – from the build quality, consistency, reliability, user experience, screen quality, quietness, etc. – no other system I have ever owned comes even close. All of our bioinformatics staff works on iMacs to work out pipelines and then log into…

Continue Reading Macbook M1 pro/M2 pro or Dell (with Ubuntu/other linux distribution) for bioinformatics stuff?

Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

Lo MT, Kauppi K, Fan CC, Sanyal N, Reas ET, Sundar VS, Lee WC, Desikan RS, McEvoy LK, Chen CH, Alzheimer’s Disease Genetics, C. Identification of genetic heterogeneity of Alzheimer’s disease across age. Neurobiol Aging. 2019;84(243):e241-243. doi.org/10.1016/j.neurobiolaging.2019.02.022. Article  Google Scholar  Nacmias B, Bagnoli S, Piaceri I, Sorbi S. Genetic heterogeneity…

Continue Reading Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer’s disease brains | Cell & Bioscience

How To Download R Studio On Mac

Introduction Welcome to the world of data analysis and statistical computing! If you’re a Mac user looking to download R Studio, you’re in the right place. R Studio is a powerful integrated development environment (IDE) that allows you to work with the R programming language, making it easier to analyze…

Continue Reading How To Download R Studio On Mac

Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

Samples for H3K27ac ChIP–seq Samples were collected by the GTEx Consortium. The donor enrollment and consent, informed consent approval, histopathological review procedures, and biospecimen procurement methods and fixation were the same as previously described22. No compensation was provided to the families of participants. Massachusetts Institute of Technology Committee on the…

Continue Reading Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease

Transposon-encoded nucleases use guide RNAs to promote their selfish spread

Siguier, P., Gourbeyre, E., Varani, A., Ton-Hoang, B. & Chandler, M. Everyman’s guide to bacterial insertion sequences. Microbiol. Spectr. 3, MDNA3-0030-2014 (2015). Article  PubMed  Google Scholar  He, S. et al. The IS200/IS605 family and “peel and paste” single-strand transposition mechanism. Microbiol. Spectr. 3, MDNA3-0039-2014 (2015). Article  ADS  Google Scholar  Kapitonov,…

Continue Reading Transposon-encoded nucleases use guide RNAs to promote their selfish spread

Rstudio – extremely slow with Stan files – RStudio IDE

I am having problems on my M2 MacBook Pro when I have Stan files open in the IDE. When having a .stan file open in the IDE everything becomes extremely slow, take a few minutes to save the Stan file, takes minutes to save a .R file, loading files, saving…

Continue Reading Rstudio – extremely slow with Stan files – RStudio IDE

How To Read Chip-Seq Data

Source: Youtube.com The era of big data has revolutionized the way we analyze and interpret complex biological systems. In the field of genomics, Chip-Seq (Chromatin Immunoprecipitation Sequencing) data has become a valuable resource for understanding gene regulation and the functionality of the genome. Chip-Seq data provides insights into the binding…

Continue Reading How To Read Chip-Seq Data

Genes with promoter and enhancer regions as GTF

Okay, first things first Please I am in hurry and need help Slow down and think again what you are doing. I used MACS Used MACS for what? (BTW, convert SAM to BAM and save some space. Just a suggestion). I’m sure you wanted to find out ChIP enriched regions,…

Continue Reading Genes with promoter and enhancer regions as GTF

Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation

Abstract Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as…

Continue Reading Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation

Paired ATAC- and RNA-seq offer insight into the impact of HIV on alveolar macrophages: a pilot study

Fitzpatrick, M. E., Kunisaki, K. M. & Morris, A. Pulmonary disease in HIV-infected adults in the era of antiretroviral therapy. AIDS 32, 277–292. doi.org/10.1097/qad.0000000000001712 (2018). Article  PubMed  Google Scholar  Brown, J. & Lipman, M. Community-acquired pneumonia in HIV-Infected individuals. Curr. Infect. Dis. Rep. 16, 397. doi.org/10.1007/s11908-014-0397-x (2014). Article  PubMed  PubMed…

Continue Reading Paired ATAC- and RNA-seq offer insight into the impact of HIV on alveolar macrophages: a pilot study

Bioinformatics Programmer in La Jolla, CA for University of California San Diego

Details Posted: 12-Sep-23 Location: La Jolla, California Salary: Open This position is a contract/limited position with the possibility of extension/career conversion. UCSD Layoff from Career Appointment: Apply by 09/13/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 09/25/2023. Eligible…

Continue Reading Bioinformatics Programmer in La Jolla, CA for University of California San Diego

Bioinformatics Programmer – 125138

This position is a contract/limited position with the possibility of extension/career conversion. UCSD Layoff from Career Appointment: Apply by 09/13/2023 for consideration with preference for rehire. All layoff applicants should contact their Employment Advisor. Special Selection Applicants: Apply by 09/25/2023. Eligible Special Selection clients should contact their Disability Counselor for…

Continue Reading Bioinformatics Programmer – 125138

Question regarding MACS2 approach of peak calling

Question regarding MACS2 approach of peak calling 0 I know the way MACS2 uses Poisson distribution to find the p value for the enrichment of a signal peak(observed) as compared to the local control signal(expected). My question is can we compare the p values of different experiments with different sequencing…

Continue Reading Question regarding MACS2 approach of peak calling

Thymic mimetic cells function beyond self-tolerance

Klein, L., Kyewski, B., Allen, P. M. & Hogquist, K. A. Positive and negative selection of the T cell repertoire: what thymocytes see (and don’t see). Nat. Rev. Immunol. 14, 377–391 (2014). Article  CAS  PubMed  PubMed Central  Google Scholar  Bornstein, C. et al. Single-cell mapping of the thymic stroma identifies…

Continue Reading Thymic mimetic cells function beyond self-tolerance

Calling large domains of signal enrichment (broad peaks) from log2,input normalized ChIP-seq data

Calling large domains of signal enrichment (broad peaks) from log2,input normalized ChIP-seq data 1 As in the title, I am looking for approaches for calling large heterochromatin domains (like Lamina-associated domains, average size ~200Mb). I would like to start from bigwig files that show the log2(IP library in CPM/input library…

Continue Reading Calling large domains of signal enrichment (broad peaks) from log2,input normalized ChIP-seq data

Why is chromHMM’s binarizeBed with the -peaks argument not recommended for broad peaks?

Why is chromHMM’s binarizeBed with the -peaks argument not recommended for broad peaks? 1 Hi! I am using publicly available data for chromatin state annotation, and building my model with chromHMM. You need to send in an application in order to get the raw data (fastq files), but the enriched…

Continue Reading Why is chromHMM’s binarizeBed with the -peaks argument not recommended for broad peaks?

python – Run command when creating Conda environment with Snakemake

I presume that downloading script produces some output. I would split your rule into two rules, one specifically for downloading and the other only for running the annotation. The downloading rule will have declared only the output directive, which would be the input for the second rule. rule download_genome: output:…

Continue Reading python – Run command when creating Conda environment with Snakemake

Knitting Issues | R Guide

Apple M1/M2 As of August 2023, it seems that there is no version of RStudio built for Apple Silicon Macs (M1/M2). To follow the progress and read some background you might want to check out this blog. In the meantime, it should work fine to use an Intel-based version of…

Continue Reading Knitting Issues | R Guide

Filtering transcription factor and HOMER and ENCODE

Filtering transcription factor and HOMER and ENCODE 0 Hello, I have a list of transcription factors identified by HOMER tool form MACS2 peak called. I want to filter this list as it has about 70 TFs. Does anyone know about ENCODE transcription factor database and how to use that database…

Continue Reading Filtering transcription factor and HOMER and ENCODE

Senior Research Associate/Associate Scientist, Cell Biology – Cambridge, Cambridgeshire, United Kingdom – CS Genetics Limited

Description Our Company CS Genetics is a privately-held genomics-technology company based in Cambridge, UK and San Diego, California. We are a nimble, highly-capable team focused on delivering genuine step-change innovation in genomic tools for research and clinical applications. We have developed a disruptive platform for single-cell genomics which leverages instrument-free,…

Continue Reading Senior Research Associate/Associate Scientist, Cell Biology – Cambridge, Cambridgeshire, United Kingdom – CS Genetics Limited

Chip-Seq and DeepTools

Chip-Seq and DeepTools 0 Hello, I have Chip-Seq data for two transcription factor (TF1,TF2) and they have significant numbers of peaks overlapped (MACS2 Peak calling) and I want to plot linear correlation between the signal of TF1 and TF2 peaks in the shared binding sites. Please guide me. Thank you…

Continue Reading Chip-Seq and DeepTools

How to get a list of gene names from macs2 peaks

How to get a list of gene names from macs2 peaks 1 Hello, I have a fairly straightforward question that is surprisingly difficult to answer (or find relevant content) online. I have used macs2 to call peaks for two samples. I have multiple output files, being .narrowPeak, .xls, and .bed…

Continue Reading How to get a list of gene names from macs2 peaks

Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma

Workflow overview CITE-seq and cell hashing were performed on liquid and solid tissue biopsies (Fig. 1a, b). Experimentally, cells from 17 samples (Supplementary Data 2) were hashed and stained with a panel of 97 antibodies (Supplementary Data 2) covering key as well as exploratory immuno-oncology markers resulting in 57,261 cells after preprocessing and…

Continue Reading Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma

ATAC seq Normalization and analysis pipeline problems

Hi all, I am following the ATACseq normalization and analysis pipeline outlined in this manuscript Reske et. al, 2020, and I am at the point of processing the MACS2 output in R. I used the following commands to specify my bamfiles, set the discard parameter to the blacklist for mm10,…

Continue Reading ATAC seq Normalization and analysis pipeline problems

No contrasts added. There must be at least two sample groups with at least three replicates.

Good morning, I’m working with ATACseq data for the fist time, and I’m using DiffBind for the Differential Accessibility Analysis, but I have this message error when I make the constrast: No contrasts added. There must be at least two sample groups with at least three replicates. I have two…

Continue Reading No contrasts added. There must be at least two sample groups with at least three replicates.

Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population | BMC Genomics

Oikonomou EK, Antoniades C. The role of adipose tissue in cardiovascular health and disease. Nat Rev Cardiol. 2019;16(2):83–99. Article  PubMed  Google Scholar  Sakers A, De Siqueira MK, Seale P, Villanueva CJ. Adipose-tissue plasticity in health and disease. Cell. 2022;185(3):419–46. Article  CAS  PubMed  Google Scholar  Sun W, von Meyenn F, Peleg-Raibstein…

Continue Reading Identifying novel regulatory effects for clinically relevant genes through the study of the Greek population | BMC Genomics

MACS2 peak calling and drug treatment

MACS2 peak calling and drug treatment 1 Hello, I have called peak for a transcription factor (say TF1) using MACS2 on a cell line with DMSO treated with two replicates and the same cell line was treated with a drug that is supposed to degrade the TF1. In DMSO treated…

Continue Reading MACS2 peak calling and drug treatment

The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation

Peng, J. et al. ‘Green revolution’ genes encode mutant gibberellin response modulators. Nature 400, 256–261 (1999). Article  CAS  PubMed  Google Scholar  Eshed, Y. & Lippman, Z. B. Revolutions in agriculture chart a course for targeted breeding of old and new crops. Science 366, eaax0025 (2019). Article  CAS  PubMed  Google Scholar …

Continue Reading The master growth regulator DELLA binding to histone H2A is essential for DELLA-mediated global transcription regulation

MACS2 parameters slocal and llocal

MACS2 parameters slocal and llocal – how are they related to open chromatin? 0 Hello everyone! I found this text from MACS2 document By default, MACS considers 1000bp for small local region(–slocal), and 10000bps for large local region(–llocal) which captures the bias from a long-range effect like an open chromatin…

Continue Reading MACS2 parameters slocal and llocal

Evolutionary histories of breast cancer and related clones

Data reporting No statistical methods were used to determine the sample size. The experiments were not randomized. Pathologists were blinded to the genetic alterations in each sample during histopathological evaluation. Participants and materials We enroled 207 female patients with breast cancer who underwent surgery at the Kyoto University Hospital and…

Continue Reading Evolutionary histories of breast cancer and related clones

Rewiring cancer drivers to activate apoptosis

Weinberg, R. A. The action of oncogenes in the cytoplasm and nucleus. Science 230, 770–776 (1985). Article  ADS  CAS  PubMed  Google Scholar  Davoli, T. et al. Cumulative haploinsufficiency and triplosensitivity drive aneuploidy patterns and shape the cancer genome. Cell 155, 948–962 (2013). Article  CAS  PubMed  PubMed Central  Google Scholar  Sanchez-Vega,…

Continue Reading Rewiring cancer drivers to activate apoptosis

RARRES2 regulates lipid metabolic reprogramming to mediate the development of brain metastasis in triple negative breast cancer | Military Medical Research

Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…

Continue Reading RARRES2 regulates lipid metabolic reprogramming to mediate the development of brain metastasis in triple negative breast cancer | Military Medical Research

Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Cell culture HCC2429 cells were a kind gift from the Hamon Center for Therapeutic Oncology Research at UT Southwestern Medical Center. The cells were grown in RPMI 1640 medium (Thermo Fisher Scientific, #11875119) with addition of 10% heat-inactivated Fetal Bovine Serum (Thermo Fisher Scientific, #10-438-026) and 1% penicillin—streptomycin (Thermo Fisher…

Continue Reading Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Cell Therapy Technologies Market Surges as Life-Changing Treatments Gain Momentum

PRESS RELEASE Published July 25, 2023 “Thermo Fisher Scientific offers a complete and integrated portfolio of solutions and services for clinical science, laboratory research, and analysis. It operates in four business segments—Life Sciences Solutions, Analytical Instruments, Specialty Diagnostics, and Laboratory Products and Services.” global cell therapy technologies market is projected…

Continue Reading Cell Therapy Technologies Market Surges as Life-Changing Treatments Gain Momentum

Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling

Coil implantation in fetal lambs We have complied with all relevant ethical regulations for animal testing. All procedures followed the Canadian Council on Animal Care guidelines and were approved by the University of Western Ontario Council on Animal Care (protocol 2010-257). Time-dated pregnant Dorset × Rideau Arcott ewes (gestational age 76 days,…

Continue Reading Decreased left heart flow in fetal lambs causes left heart hypoplasia and pro-fibrotic tissue remodeling

Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells

Bourque, G. et al. Ten things you should know about transposable elements. Genome Biol. 19, 199 (2018). Article  CAS  PubMed  PubMed Central  Google Scholar  Chuong, E. B., Elde, N. C. & Feschotte, C. Regulatory activities of transposable elements: from conflicts to benefits. Nat. Rev. Genet. 18, 71–86 (2017). Article  CAS …

Continue Reading Crosstalk between RNA m6A and DNA methylation regulates transposable element chromatin activation and cell fate in human pluripotent stem cells

Bioinformatics – Bethesda | Mendeley Careers

Job Description Overall Position Summary and Objectives Under this task order, the contractor will provide support services to satisfy the overall operational objectives. The primary objective is to provide services and deliverables through bioinformatics support services as part of an existing bioinformatics team. Minimum EducationMaster’s Resume Max Pages15 Certifications &…

Continue Reading Bioinformatics – Bethesda | Mendeley Careers

Molecular features driving cellular complexity of human brain evolution

King, M. C. & Wilson, A. C. Evolution at two levels in humans and chimpanzees. Science 188, 107–116 (1975). Article  ADS  CAS  PubMed  Google Scholar  Konopka, G. et al. Human-specific transcriptional networks in the brain. Neuron 75, 601–617 (2012). Article  CAS  PubMed  PubMed Central  Google Scholar  Liu, X. et al….

Continue Reading Molecular features driving cellular complexity of human brain evolution

Organization of the human intestine at single-cell resolution

Tissue collection and processing This study complies with all relevant ethical regulations and was approved by the Washington University Institutional Review Board and the Stanford University Institutional Review Board. Human bowel tissues were procured from deceased organ donors. Written informed consent was obtained from the next-of-kin for all donor participants….

Continue Reading Organization of the human intestine at single-cell resolution

Does sequencing depth influencing ATAC peak calling?

Does sequencing depth influencing ATAC peak calling? 0 Hi All, I was wondering if anyone had experience regarding different depths of sequencing (for ATAC sequencing) and the number of peaks you would expect to be called by HMMRATAC or MACS2/3. We have done a trial run of some atac sequencing…

Continue Reading Does sequencing depth influencing ATAC peak calling?

Cancers | Free Full-Text | A Novel Bispecific Antibody for EpCAM-Directed Inhibition of the CD73/Adenosine Immune Checkpoint in Ovarian Cancer

1. Introduction Typically, tumors in patients with ovarian cancer (OC) are often diagnosed at an advanced stage [1]. Currently, cytoreductive therapy with platinum-based chemotherapy is the mainstay of disease management, to which the majority of patients with OC initially respond. Unfortunately, 70% of these patients eventually develop refractory recurrences [2]….

Continue Reading Cancers | Free Full-Text | A Novel Bispecific Antibody for EpCAM-Directed Inhibition of the CD73/Adenosine Immune Checkpoint in Ovarian Cancer

many more ChIP-seq peaks called in 1 condition than the other

many more ChIP-seq peaks called in 1 condition than the other 0 Hello everyone! We do ChIP-seq across 2 conditions each with 2 replicates. The number of called narrow peaks (MACS2 2.2.7.1, FDR < 0.1) are: cond_1-1: 8,915 cond_1-2: 10,099 cond_2-1: 1,446 cond_2-2: 801 At first, I suspected that there…

Continue Reading many more ChIP-seq peaks called in 1 condition than the other

G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions

Jiang, C. & Pugh, B. F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161–172 (2009). Article  CAS  PubMed  PubMed Central  Google Scholar  Fenouil, R. et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399–2408…

Continue Reading G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions

A human proteogenomic-cellular framework identifies KIF5A as a modulator of astrocyte process integrity with relevance to ALS

Human interactome and network-based expansion For the human interactome, we selected STRING v11.0 (combined score > 0.75), BioGRID (v 3.5.172) and IntAct (May 2019) databases derived from high-throughput studies (reporting at least 1,000 interactions). All nodes were mapped to Ensembl gene (ENSG) identifiers, edges were considered as non-directed connections and…

Continue Reading A human proteogenomic-cellular framework identifies KIF5A as a modulator of astrocyte process integrity with relevance to ALS

SEACR and MACS2

SEACR and MACS2 1 Hello everyone, I have done cut&run for a transcription factor in a mutant cell line (mutant for mentioned transcription factor as a control). I did peak calling using MACS2, as expected few peaks were called in both the replicate. When I repeat this using SEACR, in…

Continue Reading SEACR and MACS2

merging bam file

merging bam file 0 Hello everyone! I have done two independent chipseq for a transcription factor with two replicate in each experiment. I want to merge the bam file of replicates but I do not know what condition is required for merging bam file. Every replicate file has different sequencing…

Continue Reading merging bam file

Stream RStudio: A Powerful IDE for R Programming on macOS from Ofysimidydy1975

published on 2023-06-22T19:08:37Z r studio download mac Download climmulponorc.blogspot.com/?c=2uocTB R is maintained by an international team of developers who make the language available through the web page of The Comprehensive R Archive Network. The top of the web page provides three links for downloading R. Follow the link that describes…

Continue Reading Stream RStudio: A Powerful IDE for R Programming on macOS from Ofysimidydy1975

Calculate Computational Efficiency of Deep Learning Models with FLOPs and MACs

    FLOPs (Floating Point Operations) and MACs (Multiply-Accumulate Operations) are metrics that are commonly used to calculate the computational complexity of deep learning models. They are a fast and easy way to understand the number of arithmetic operations required to perform a given computation. For example, when working with…

Continue Reading Calculate Computational Efficiency of Deep Learning Models with FLOPs and MACs

Peak calling a general bed file (not reads)

Peak calling a general bed file (not reads) 0 Hi, I have a bed file of annotated regions. I want to find genomic regions which are particularly dense with these annotations. I thought perhaps a way to do this is standard peak calling (Poisson model) and I was wondering if…

Continue Reading Peak calling a general bed file (not reads)

NABI MSc, PhD Bioinformatics, Agriculture, Biotech, Biochem, Life Sciences Jobs

NABI Bioinformatics, Agriculture, Biotech, Biochem, Life Sciences Jobs For MSc, PhD – Attend Walk-In Don’t forget to check out possible interview questions for this job below 18Days11Hours09Minutes48Seconds National Agri-Food Biotechnology Institute (NABI)(Dept. of Biotechnology, Ministry of Science & Technology, Govt. of India)Sector-81, Knowledge City, Manauli P.O, S.A.S. Nagar-140306, Punjab, India.Website:…

Continue Reading NABI MSc, PhD Bioinformatics, Agriculture, Biotech, Biochem, Life Sciences Jobs

Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei

Dahl, K. N., Ribeiro, A. J. S. & Lammerding, J. Nuclear shape, mechanics, and mechanotransduction. Circ. Res. 102, 1307–1318 (2008). Article  CAS  PubMed  PubMed Central  Google Scholar  Alisafaei, F., Jokhun, D. S., Shivashankar, G. V. & Shenoy, V. B. Regulation of nuclear architecture, mechanics, and nucleocytoplasmic shuttling of epigenetic factors…

Continue Reading Chromatin reprogramming and bone regeneration in vitro and in vivo via the microtopography-induced constriction of cell nuclei

seq – Texas A&M HPRC

Back to Bioinformatics Main Menu MACS GCATemplates available: ada MACS homepage module spider MACS Model-based Analysis of ChIP-Seq data. MACS2 GCATemplates available: no MACS2 homepage module spider MACS2 Model-based Analysis of ChIP-Seq data. SICER GCATemplates available: ada SICER homepage module spider SICER A clustering approach for identification of enriched domains from histone modification ChIP-Seq data ChIP-Seq…

Continue Reading seq – Texas A&M HPRC

Scientists unlock virus-fighting power with synthetic nanobody platform

In a recent study published in the Proceedings of the National Academy of Sciences, researchers developed a fully synthetic platform for nanobody generation. Study: Fully synthetic platform to rapidly generate tetravalent bispecific nanobody–based immunoglobulins. Image Credit: Adao / Shutterstock.com What are nanobodies? Biologics have been increasingly used for the treatment or prevention…

Continue Reading Scientists unlock virus-fighting power with synthetic nanobody platform

Programming Processors In Heterogeneous Architectures

Programming processors is becoming more complicated as more and different types of processing elements are included in the same architecture. While systems architects may revel in the number of options available for improving power, performance, and area, the challenge of programming functionality and making it all work together is turning…

Continue Reading Programming Processors In Heterogeneous Architectures

Heritable transcriptional defects from aberrations of nuclear architecture

Cell culture and cell line construction Cells were cultured at 37 °C in 5% CO2 atmosphere with 100% humidity. Telomerase-immortalized RPE-1 retinal pigment epithelium cells (CRL-4000, American Type Culture Collection), U2OS osteosarcoma cells (HTB-96, American Type Culture Collection) and derivative cell lines were grown in DMEM/F12 (1:1) medium without phenol red…

Continue Reading Heritable transcriptional defects from aberrations of nuclear architecture

Sexual differentiation in human malaria parasites is regulated by competition between phospholipid metabolism and histone methylation

Drakeley, C., Sutherland, C., Bousema, J. T., Sauerwein, R. W. & Targett, G. A. T. The epidemiology of Plasmodium falciparum gametocytes: weapons of mass dispersion. Trends Parasitol. 22, 424–430 (2006). Article  PubMed  Google Scholar  Kafsack, B. F. C. et al. A transcriptional switch underlies commitment to sexual development in malaria…

Continue Reading Sexual differentiation in human malaria parasites is regulated by competition between phospholipid metabolism and histone methylation

Bioinformatics job with E-talentnetwork | 1401831339

Job Description Overall Position Summary and Objectives Under this task order, the contractor will provide support services to satisfy the overall operational objectives. The primary objective is to provide services and deliverables through bioinformatics support services as part of an existing bioinformatics team. Minimum EducationMaster’s Resume Max Pages15 Certifications &…

Continue Reading Bioinformatics job with E-talentnetwork | 1401831339

Discover the Best 8 AI Tools for Developers To Automate & Improve Efficiency

As the world of technology continues to evolve at an incredible pace, it’s no surprise that Artificial Intelligence (AI) has become an integral part of the industry. AI-powered tools  have become ubiquitous utilities  for developers across a wide range of industries. From automating mundane tasks to creating cutting-edge applications, AI…

Continue Reading Discover the Best 8 AI Tools for Developers To Automate & Improve Efficiency

MACS2 peak calling

MACS2 peak calling 1 Hi all! I have performed peak calling using MACS2. Is it correct that the bed file has not strand of the peak? Thank you very much for your help MACS2 peak-calling • 113 views Yes, that is correct. Peaks from experiments such as ChIP-seq or ATAC-seq…

Continue Reading MACS2 peak calling

Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation

Vogel, B. et al. The Lancet women and cardiovascular disease Commission: reducing the global burden by 2030. Lancet 397, 2385–2438 (2021). Article  PubMed  Google Scholar  Adlam, D., Alfonso, F., Maas, A., Vrints, C. & Writing Committee. European Society of Cardiology, acute cardiovascular care association, SCAD study group: a position paper…

Continue Reading Genome-wide association meta-analysis of spontaneous coronary artery dissection identifies risk variants and genes related to artery integrity and tissue-mediated coagulation

Ask HN: What is a AI chip and how does it work?

Apple Silicon Macs have special matrix multiplication units (AMX) that can do matrix multiplication fast and with low energy requirements [1]. These AMX units can often beat matrix multiplication on AMD/Intel CPUs (especially those without a very large number of cores). Since a lot of linear algebra code uses matrix…

Continue Reading Ask HN: What is a AI chip and how does it work?

Chipseq data peak calling issue

Hi , I’m trying to do analysis of chipseq data . I have 3 samples Sample1 , sample2 and input I have done QC and then alignment using Bowtie . After that I used samtool to get bam files . Then I have used Picard for duplicate removal. Now I…

Continue Reading Chipseq data peak calling issue

High-Throughput Cardiotoxicity Screening Using Mature Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Monolayers

This protocol is significant because it enables researchers to mature commercial or in-house-made hiPSC-CMs to an adult-like phenotype that significantly improves the predictive value of hiPSC-CMs in cardiotoxicity screening. The main advantage of this protocol is that it delivers mature hiPSC-CMs in a high throughput format for optical mapping of…

Continue Reading High-Throughput Cardiotoxicity Screening Using Mature Human Induced Pluripotent Stem Cell-Derived Cardiomyocyte Monolayers

How to improve signal to noise ratio in sequencing samples?

How to improve signal to noise ratio in sequencing samples? 1 Hi everyone! I’m dealing with NGS data derived from CUT&TAG experiments and I’m quite new to the field. I ended up with very noisy IGV profiles and sample coming from my antibody of interest looks like my IgG one….

Continue Reading How to improve signal to noise ratio in sequencing samples?

Encode project signal p-value

Encode project signal p-value 0 In TF ChIP-Seq experiments, ENCODE project provides two types of signal BigWig files: fold change over control and signal p-value. I’m unable to locate the specific pipeline for creating the signal p-value BigWig files. Although MACS2 is mentioned, it appears that the resulting BigWig file…

Continue Reading Encode project signal p-value