Tag: MACS

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…

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…

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…

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…

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 &…

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…

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…

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…

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…

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…

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…

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….

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…

Abstract Background: Intrahepatic cholangiocarcinoma (ICC) is a malignant tumor, which poses a serious threat to human health. Histone 3 lysine 9 trimethylation (H3K9me3) is a post-translational modification involved in regulating a broad range of biological processes and has been considered as potential therapeutic target in types of cancer. However, there…

CUT&Tag data processing: peak caller choice and typical peak size profile 1 Greetings everyone, I am currently analysing CUT&Tag data (a recent technique, variant of the ChIP-seq), capturing different histone variants. To do so, I tried all the different suggested tools for peaks calling: the more general MACS2 (broad peaks,…

Question on removing duplicates with ATAC-Seq and ChIP-Seq 0 Hi I am new to ATAC-Seq and ChIP-Seq and I have a question on removing duplicates when it comes to paired-end ATAC-Seq and paired-end ChIP-Seq pipelines. I have seen some papers where clumpify is used in the first step to remove…

MACS2 , heatmap 0 Hello guys, I am doing cut&run analysis for some transcription factors and I have three replicates of BAM files and three replicates of MACS2 output. For downstream studies should I merge three replicates of bam file to plot heatmap? In case replicates are not highly correlated…

ChIP-seq is a method for identifying genome-wide transcription factor-DNA association. It uses chromatin immunoprecipitation with massively parallel short-read sequencing, which allows for high sensitivity, specificity, and spatial resolution. However, analyzing ChIP-seq data presents new challenges due to the complexity of the biological systems and variability in sequence data. The authors…

Hello, I’m currently following this paper Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. It is a ChIP-Seq to generate genome-wide maps of 34 chromatin modifications (17 acetylation marks, and 17 methylation marks) and the histone variant H2AZ. B cells were either naïve (G0) or activated for…

Cut&Run and heatmap 0 Hello guys, I am doing cut&run analysis from some transcription factors and I have three replicate for each sample. After bowtie2 alignment and MACS2 Peakcalling individually for each sample I need not plot heatmap. I have three replicates of BAM files and three replicates of MACS2…

Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….

ATAC-seq peak calling with MACS 3 I am trying to call peaks in ATAC-seq data. Not surprisingly, MACS is a popular option. According to the MACS documentation: To find enriched cutting sites such as some DNAse-Seq datasets. In this case, all 5′ ends of sequenced reads should be extended in…

MACS2 and BED file 0 I have run bowtie2 and then bam file sorted by name was converted to bed file after removing mitochondrial DNA and random sequences. When I use blacklisted regions bed file to filter my bed file it shows error. The error is that many rows in…

Producing ATAC count matrix for multiple samples 0 Hi All I’ve just been trying to analyse some ATAC-Seq data and have got a little stuck. I’m relatively new to bioinformatics and ATAC seems like a bit of a step up from RNASeq analysis! My data are ATAC-Seq reads from 6…

Confused with macs has a same result when my input files are BED 3 and BED 5 format 0 so first i using BED 5 format which has a score column to call peak: chr10 3101187 3101287 . 2 + chr10 3101479 3101579 . 12 + chr10 3108149 3108249 ….

Apple has made waves with its transition from intel processors to its own M-series chips. This shift has a lot of tech enthusiasts and industry experts speculating about its impact on the future of computing. Apple had previously been making their own processors for their mobile devices, such as iPhones…

Anantharaman V, Koonin EV, Aravind L. Comparative genomics and evolution of proteins involved in RNA metabolism. Nucleic Acids Res. 2002;30:1427–64. doi.org/10.1093/nar/30.7.1427. Article  CAS  PubMed  PubMed Central  Google Scholar  Fernández-Moya SM, Estévez AM. Posttranscriptional control and the role of RNA-binding proteins in gene regulation in trypanosomatid protozoan parasites. Wiley Interdiscip Rev…

DiffBind missing peaks and FRiP 2 I noticed that when I first read in my sample sheet, I get a DBA object with 1226 sites (consensus peaks), yet after running dba.count() on this same object, it is down to 1188 sites. I did not apply any blacklists/greylists. Also, the FRiP…

Diffbind dba.count doesn’t give FRiP score 1 Hi I am completely new to DiffBind, R and programming in general. I want to use diffbind to analyze peaks called with macs2. When I use dba.count(), I can not get FRiP score at all. I googled this question, but didn’t work. Here…

*Important notice: bioRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, which is otherwise known as the coronavirus disease 2019 (COVID-19), continues to pose significant…

First (and last?) time running qiime. All I am trying to do at the moment is demultiplex. Qiime cutadapt is unable parse my metadata file no matter what I do to it. I’ve spent hours trying to fix this ridiculous bug. It seems most likely that the cutadapt plugin isn’t…

Tutorial:ChIP-Seq Analysis Tutorial 0 For those who aren’t familiar with this technique, ChIP-Seq refers to chromatin immunoprecipitation followed by next generation sequencing (NGS). It is used to find DNA-protein binding, such as transcription factor binding sites, histone modification, open chromatin regions, and more. The core idea behind each of these…

Knockdown of LFPRLR reduces splenic B-cell subsets in SLE-prone mice To investigate whether the PRL-LFPRLR axis raises the risk of initiation of B-cell malignancies, we compared SLE-prone MRL-lpr mice treated with either control SMO or LFPRLR SMO. Among SLE-prone models, we chose MRL-lpr mice because they accumulate genetic lesions indicative…

Bergwerk, M. et al. Covid-19 breakthrough infections in vaccinated health care workers. N. Engl. J. Med. 385, 1474–1484 (2021). Article  CAS  PubMed  Google Scholar  V’Kovski, P., Kratzel, A., Steiner, S., Stalder, H. & Thiel, V. Coronavirus biology and replication: implications for SARS-CoV-2. Nat. Rev. Microbiol. 19, 155–170 (2021). Article  PubMed …

macs2 for centromere chip-seq peak calling 0 I am trying to locate the centromere in one of our genome assemblies using chip-seq data from CenH3. I am performing the peak calling using macs2 peakcall function using bam files from bowtie2 (treatment and control). I am using the narrowPeak file from…

How to annotate a MACS2 peak output file that is in tabular format? 0 I am fairly new to ChIP-seq analysis. I am using data from someone else and they only have the MACS2 peak file in tabular format. I have annotated peaks previously using MACS2 .bed files using ChIPseeker,…

1 is not found in chromosome sizes file 0 I am trying to convert bedGraph to bigWig file with bedGraphToBigWig. but I always get “1 is not found in chromosome sizes file”. I used the following script macs2 callpeak -c SRRc_sorted.bam -t SRRe_sorted.bam -B –nomodel –extsize 200 –SPMR -q 0.01…

I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I’m trying to first annotate the peaks the way that the authors did in the publication. This is what they say they did – “Gene annotation of the regions bound by indicated proteins were performed…

I am using ChIPseeker to annotate MACS2 peaks files from publicly available data. To begin, I’m trying to first annotate the peaks the way that the authors did in the publication. This is what they say they did – “Gene annotation of the regions bound by indicated proteins were performed…

Merge replicates for CHIP-seq analysis 0 I am performing for the first time CHIP-seq analysis with two replicas, I used MACS2 to find the peaks of the two respective replicas, I used IDR to find the percentage of peaks in common and bedtools intersect to get a bed file that…

Almost no peak output after peakcalling of mtDNA with MACS2 0 I am new to the CHIP-seq analysis. I am basically trying to call peaks using MACS 2 with the proccessed data of mitochondrial DNA only in bedgraph format given in the accession number GSE48176 under the link www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48176. I…

Hello I have been using DiffBind to perform differential enrichment analysis on my ChIP-seq dataset where I have 2 sample groups, WT and KO, with 4 replicates in each sample group. The analysis reports only 2 significantly differential enriched peaks at FDR < 0.05, and the situation does not change…

Starzl TE. The early days of transplantation. JAMA. 1994;272(21):1705. Article  CAS  PubMed  PubMed Central  Google Scholar  Vanholder R, Dominguez-Gil B, Busic M, Cortez-Pinto H, Craig JC, Jager KJ, et al. Organ donation and transplantation: a multi-stakeholder call to action. Nat Rev Nephrol. 2021;17(8):554–68. Article  PubMed  PubMed Central  Google Scholar  Aubert…

Overview Product name Sample type Tissue, Adherent cells, Suspension cells Assay time 7h 00m Product overview ab185908 is a complete set of reagents required for carrying out a successful ChIP-Seq starting from mammalian…

Lentiviral vector construction and production The lentiviral vector was designed as previously described [13, 41]. LdCV vector contains the following: human codon-optimized S. pyogenes dCas9 which was fused at the C-terminus with VP64-p65-Rta (VPR). LAT-TCS-dCas9-VPR was assembled by fusing LAT (Human cDNA, NM_001014987.2) with dCas9-VPR-Q8 and cloned into a modified…

Reagents and resources All the reagents including qPCR primers, antibodies, and software used are listed in Supplementary Table 1 ESC maintenance Human embryonic stem cell (H7-hESCs; WiCell, Madison, WI, www.wicell.org) reporter line with CRISPR-engineered multicistronic BRN3B-P2A-tdTomato-P2A-Thy1.2 construct into the endogenous RGC specific BRN3B locus was used for isogenic control20. CRISPR mutated…

How to do Binding and Expression Target Analysis? 0 Hello I used BETA to infer direct target genes from ChIP-seq peaks. Can someone help to let me know what is wrong with the program? I can not get feedback from GitHub. Is there a similar tool that can do the…

Chip-seq Analysis 0 Hi everyone, I am analyzing chipseq data and I am trying to figure out the handling of biological replicates and the best tools to use. I tried to dig into the former questions, but it is hard to navigate thorough so many information. I have 2 different…

cwang February 21, 2023, 12:04am 1 Hi, I’m trying to learning analysis by following various tutorials and when using scvi to predict doublets, my kernel keeps dying. This is the code that I’m trying to run scvi.model.SCVI.setup_anndata(adata) vae = scvi.model.SCVI(adata) vae.train() There was post about this same issue and two…

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249 (2021). Article  PubMed  Google Scholar  Sanli, O. et al. Bladder cancer. Nat. Rev. Dis. Prim. 3, 17022 (2017). Article  PubMed  Google Scholar  International…

MACS to Signac 1 Hey guys– Once MACS is completed running, how would I feed the peaks/bed file into Signac for each sample up to merging and finally clustering? I believe the vignette only demonstrates if one were to add *fragment files and I need the peaks file from MACS…

MACS Error 1 I’m currently running MACS2 and have the following error: $ macs2 callpeak -f BAMPE -t READS.bed -g hs -n test -B -q 0.01 . . . . **(MACS2/IO/Parser.c:12841)struct.error: unpack requires a string argument of length 4** Any suggestions? I’ve run and re-run this to no avail. scatac-seq…

Help with MACS2 installation errors 0 Hi, I am trying to install MACS2 in server. I already installing Anaconda with python3 and successfully installed MACS3 with > pip install MACS3 However, when I trying to install MACS2 with same pip command it failed. (base) wkq953@porus01:~> pip install MACS2 –user Collecting…

Much less peaks compared to other replicates 0 Hi! I’m doing ATAC-seq data analysis now. There’re 3 replicates in one condition. However, I got much less peaks in a replicate under a certain condition. Compared to other replicates in this condition, only 1719 peaks were called in this replicate (more…

A2Mcap measures protease activity by covalent substrate trapping The principle behind A2Mcap is the formation of a covalent bond between a protease of interest and a modified A2M substrate. A covalent bond is formed if a protease cleaves the A2M bait sequence, which triggers a structural rearrangement in A2M and…

Biosafety statement All experiments with cell lines and viral infections were carried out in a Biosafety Level 2 facility under the approval of the Biosafety Office in the Department of Environment, Health and Safety and the Institutional Biosafety Committee at the University of North Carolina at Chapel Hill. The laboratory…

Using bigWigCompare to correct for input signal 0 I’m trying to visualize differences in H3K9ac binding between treatment and control groups for a certain project through visualizing the profile plots, but the provided files are only BED files with significant peak coordinates, raw SRA runs and a couple of BigWig…

scATAC-seq workflow 0 Help. I am still new to the concept of scATAC-seq and was wondering if anyone could provide a straightforward workflow. I am referring to the Signac vignettes but it seems to go back and forth between tutorials. I am starting out with 2 samples– one knockout and…

Ethics statement All fresh peripheral blood samples were obtained after approval of protocols by the Weizmann Institutional Review Board (IRB application 92-1) and following informed consent from the donors. The study using BAL fluid samples was approved by the Hadassah Medical Organization research ethics committee in accordance with the Declaration…

CoveragePlot in Signac from MACS2 Object 0 I am currently trying to produce a CoveragePlot() to locate a number of transcription factors; however instead of the input being a Chromatin Assay or Seurat Object, I wanted to pass output files passed by MACS2 which was run in the terminal. I…

Differential Peak Analysis for a specific gene using only bigWig + BED files? 0 I’m trying to analyze a public dataset (GEO accession: GSE66318) which stems from a CHIP-Seq analysis by Vasudevan et al. 2015. Specifically, I’m interested in the peak-calling results they provide for the acetylation marks for both…

Hall, B. K. & Wake, M. H. in The Origin and Evolution of Larval Forms (eds Hall, B. K. & Wake, M. H.) 1–19 (Academic Press, 1999). Nielsen, C. Animal phylogeny in the light of the trochaea theory. Biol. J. Linn. Soc. 25, 243–299 (2008). Article  Google Scholar  Garstang, W….

Unknown chromosome results in .narrowPeak files 1 I’ve run macs2 callpeaks and in the .narrowPeak file I have many rows for chromosomes with names like “chrUn_KI270522v1”. Can anyone tell me what this means? The peak was found in an unknown chromosome? Is this due to noise and can be ignored?…

Extracting list of target genes from ChIP-seq bigwig file 1 I am reading a publication where the authors performed ChIP-seq on a specific TF. Their data was deposited on NCBI in bigwig format. I would like to extract the final list of target genes. Is this possible using the bigwig…

Therapeutic mRNAs can be stabilized by the incorporation of modified nucleosides, synthetic capping, and the addition of lengthy poly-A tails, and can be enhanced with codon optimization (1113). Maintains viability . Plant tissue culture is a collection of techniques used to maintain or grow plant cells, tissues or organs under…

Review . 2022 Feb 3;5(1):pbac004. doi: 10.1093/pcmedi/pbac004. eCollection 2022 Mar. Affiliations Expand Affiliations 1 Department of Cell Biology, Naval Medical University, Shanghai 200433, China. 2 Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, and Guangdong Provincial Key Laboratory of Single Cell Technology and Application, Southern Medical University,…

Clapier, C. R., Iwasa, J., Cairns, B. R. & Peterson, C. L. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat. Rev. Mol. Cell Biol. 18, 407–422 (2017). CAS  PubMed  PubMed Central  Article  Google Scholar  Mashtalir, N. et al. Modular organization and assembly of SWI/SNF family chromatin remodeling complexes….

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

Hi all,I have been using pymc3 for about a year. A few months ago I changed from an intel mac to an M1 mac. Suddenly, I can’t use pymc3 anymore. I keep getting the following error that I have no idea how to interpret: You can find the C code…

Using a Mac with M1 chip, I’m trying to install the following Bioconda packages: cutadapttrim-galoresamtoolsbedtools.htseq.bowtie2.deeptools.macs2 I’ve been able to install picard and fastqc with no issues, but all others turn out one of two error messages: PackagesNotFoundError: The following packages are not available from current channels: or Found conflicts! Looking…

INTRODUCTION Mammalian life starts with the fusion of two terminally differentiated gametes, sperm and oocyte, resulting in a totipotent zygote. After going through preimplantation development, the zygote reaches blastocyst before implantation. The two most important events taking place during preimplantation development are zygotic genome activation (ZGA) and the first cell…

Job Posting for Bioinformatics Scientist at Alpine Immune Sciences Alpine Immune Sciences is applying our platform discovery technology to bring innovative new therapies to people living with serious or life-threatening illnesses or conditions, such as cancer and autoimmune/inflammatory diseases. Exciting challenges lie ahead—guided by our core values, we’ll…

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

I am having issues running MACS3. I installed MACS3 using: wget github.com/macs3-project/MACS/archive/refs/tags/v3.0.0a6.tar.gz tar -xf v3.0.0a6.tar.gz chmod a+rwx MACS-3.0.0a6/bin/macs3 It appears to be installed correctly because the following code generates the predictd help window: MACS-3.0.0a6/bin/macs3 predictd –help However, when I try running the actual code I get the following error: MACS-3.0.0a6/bin/macs3…

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….

R CODER’s Projects awesome-ggplot2 A curated list of awesome ggplot2 tutorials, packages etc. awesome-R A curated list of awesome R packages, frameworks and software. Awesome-R-packages A curated list 📄 of awesome 🌟 R packages 🌟 (WORK IN PROGRESS) calendR Ready to print calendars with ggplot2 chinchet A geom for adding…

Getting peak heights from TF chIP-seq data (wig file) 1 Hello everyone, I have TF ChIP seq data from NCBI GEO in wig format. I converted wig to bedgraph and then used MACS peak caller to get bed narrowpeak files.I further uploaded file on genome browser to get graphical map…

Name Last modified Size Description Parent Directory   –   Pc.consensus_peaks.annotatePeaks.txt 30-Mar-2021 19:12 1.6M   Pc.consensus_peaks.bed 30-Mar-2021 19:12 376K   Pc.consensus_peaks.boolean.annotatePeaks.txt 30-Mar-2021 19:12 2.4M   Pc.consensus_peaks.boolean.intersect.plot.pdf 30-Mar-2021 19:12 5.5K   Pc.consensus_peaks.boolean.intersect.txt 30-Mar-2021 19:12 91   Pc.consensus_peaks.boolean.txt 30-Mar-2021 19:12 1.2M   Pc.consensus_peaks.featureCounts.txt 30-Mar-2021 19:12 464K   Pc.consensus_peaks.featureCounts.txt.summary 30-Mar-2021 19:12 458  …

  A new publication describes and update to AutoDock Vina “AutoDock Vina 1.2.0: New Docking Methods, Expanded Force Field, and Python Bindings” DOI. AutoDock Vina is arguably one of the fastest and most widely used open-source programs for molecular docking. However, compared to other programs in the AutoDock Suite, it…

1. Yin H, Price F, Rudnicki MA. Satellite cells and the muscle stem cell niche. Physiol Rev. 2013;93(1):23–67. CAS  PubMed  PubMed Central  Google Scholar  2. Hoppeler H, Fluck M. Plasticity of skeletal muscle mitochondria: structure and function. Med Sci Sport Exer. 2003;35(1):95–104. CAS  Google Scholar  3. Astruc T: Carcass Composition,…

Piranha Peak-Calling with multiple replicates 0 I am trying to call RNA-Protein interation peaks by using Piranha software. I have multiple replicates for each experiment and the control data, and I can’t seem to understand how to combine them into one Piranha query. For example, if I was to call…

Macbook Pro or PC laptop for bioinformatics? 3 I would like to be able to run most any of the typical ChIP-seq and RNA-seq tools (e.g. MACS2) from a home laptop computer; in other words, without access to HPC. I will be working with data from the relatively small eukaryotic…

Calculating area under the curve for broad peaks from ChIP-seq 0 Hello all, My first time posting on Biostars. We are analyzing the distribution of RNA polymerase across a Plasmodium genome. The distribution, as you might imagine, is broad, spanning entire genes and beyond. We have used MACS2 “corrected” for…

difference between treat_pileup and bdgcmp fold enrichment tracks macs2 0 Hello, I created bigwig file from a treat_pileup.bdg file generated by macs2 and also used treat_pileup.bdg and control_lambda.bdg with macs2 bdgcmp. Here is my codes; macs2 callpeak -t sample.bam -c sample_input.bam -g hs -f BAM -q 0.001 –bdg –outdir /folder…

Identical peak coverage in IP bam file and Input bam file 0 Hi, I had ChIP seq data that I aligned using STAR and got the bam files for and ran peak calling using macs2. I see a list of regions that are enriched, however, when I use the bam…

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…

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…

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…

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…

DOI: 10.18129/B9.bioc.MACSdata     Test datasets for the MACSr package Bioconductor version: Release (3.13) Test datasets from the MACS3 test examples are use in the examples of the `MACSr` package. All 9 datasets are uploaded to the `ExperimentHub`. The original data can be found at: github.com/macs3-project/MACS/. Author: Qiang Hu [aut,…

I am using Diffbind to call differential peaks on an ATAC seq dataset of four conditions (AW, BW, B, and C), and each condition has 2 replicates. One of my replicates (BW2) has low quality (low number of peaks detected by MACS2 compared to the other replicate, and low FRiP)….

Introduction Mirror-image pain (MIP) is a mysterious pain phenomenon which is accompanied with many clinical pain conditions.1 MIP develops from the healthy body region which is contralateral to the actual injured site.1–3 MIP is typically characterized by increased mechanical hypersensitivity on the uninjured mirror-image body side.4 It can be triggered…

Can I use the summits.bed from MACS2 on HOMER 1 I understand that to run HOMER you need BED files, so could I use the BED output file from “macs2 callpeak” to run “findMotifsGenome.pl”? Homer Macs callpeak bed • 40 views • link updated 2 hours ago by seidel 8.3k…

Using MACS2 parameters 0 Trying to reproduce a galaxy training in Linux CLI. I’ve come up with the following commands for the peak calling with MACS2. Am I on the right track? The galaxy parameters are- macs2 command can be- macs2 callpeak -t input_file.bed -n macs_output -g 50818468 –nomodel –shift…

How to use IGV (or any genome vis tool) show normalised ChIP-Seq peak intensity? 1 Hi everyone: I have a question about IGV, I am quite new on ChIP-seq data. Question: In analysis side, I use MACS2 for peak calling, MAnorm2 for normalisation. etc, the result looks good. In IGV…

Compare bedgraphs of two treatments after MACS2 callpeak . Output Files of MACS2 bdgdiff . Hello everyone, I have some bedgraph files from a ChIP- … Source link

callpeak: Main MACS2 Function to Call peaks from alignment results. bdgpeakcall: Call peaks from bedGraph output. bdgbroadcall: Call broad peaks … Source link

MACS2 bdgcmp for two bedgraph peak callingKeep it as 1.0 or default in most … bdgcmp Deduct noise by comparing two signal tracks in bedGraph. Source link

MACS2 bdgcmp for two bedgraph peak calling Mar 16, 2015 · I have the data in Bedgraph. MACS2 can use bedgraph as input for peak calling. Source link

Signac CallPeaks from multiple fragment files 0 I am attempting to run Macs2 CallPeaks on some multiome data and running into a problem when attempting to run CallPeaks command on multiple fragment file paths in Seurat object. peaks<-CallPeaks(DataCombined, macs2.path = “/anaconda3/bin/macs2”) FileNotFoundError: [Errno 2] No such file or directory: ‘/Users/Desktop/multiome/sc291/atac_fragments.tsv.gz…