Tag: MACS

advantages of electroporation

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…

Continue Reading advantages of electroporation

Tumorigenicity risk of iPSCs in vivo: nip it in the bud

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,…

Continue Reading Tumorigenicity risk of iPSCs in vivo: nip it in the bud

SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

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….

Continue Reading SMARCE1 deficiency generates a targetable mSWI/SNF dependency in clear cell meningioma

A genome-scale screen for synthetic drivers of T cell proliferation

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…

Continue Reading A genome-scale screen for synthetic drivers of T cell proliferation

Pymc3 linker error – v3

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…

Continue Reading Pymc3 linker error – v3

python – Packages Not Found Error: Not available from current channel- Bioconda

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…

Continue Reading python – Packages Not Found Error: Not available from current channel- Bioconda

Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

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…

Continue Reading Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

Bioinformatics Scientist Job Opening in Seattle, WA at Alpine Immune Sciences

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…

Continue Reading Bioinformatics Scientist Job Opening in Seattle, WA at Alpine Immune Sciences

The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

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…

Continue Reading The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Issue running MACS3

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…

Continue Reading Issue running MACS3

Decoding gene regulation in the fly brain

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….

Continue Reading Decoding gene regulation in the fly brain

R-CoderDotCom | RCoderWeb – Github Help

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…

Continue Reading R-CoderDotCom | RCoderWeb – Github Help

Getting peak heights from TF chIP-seq data (wig file)

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…

Continue Reading Getting peak heights from TF chIP-seq data (wig file)

Index of /agalicina/2021/dros/chipseq/paired-end/macs/narrowPeak/consensus/Pc

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  …

Continue Reading Index of /agalicina/2021/dros/chipseq/paired-end/macs/narrowPeak/consensus/Pc

AutoDock Vina 1.2.0 | Macs in Chemistry

  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…

Continue Reading AutoDock Vina 1.2.0 | Macs in Chemistry

Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells | BMC Genomics

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,…

Continue Reading Genome-wide identification of enhancers and transcription factors regulating the myogenic differentiation of bovine satellite cells | BMC Genomics

Piranha Peak-Calling with multiple replicates

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…

Continue Reading Piranha Peak-Calling with multiple replicates

Macbook Pro or PC laptop for bioinformatics?

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…

Continue Reading Macbook Pro or PC laptop for bioinformatics?

Calculating area under the curve for broad peaks from ChIP-seq

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…

Continue Reading Calculating area under the curve for broad peaks from ChIP-seq

difference between treat_pileup and bdgcmp fold enrichment tracks macs2

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…

Continue Reading difference between treat_pileup and bdgcmp fold enrichment tracks macs2

Identical peak coverage in IP bam file and Input bam file

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…

Continue Reading Identical peak coverage in IP bam file and Input bam file

low FRiP(Fraction of Reads in Peaks) score in ATAC-seq

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…

Continue Reading low FRiP(Fraction of Reads in Peaks) score in ATAC-seq

Calling differential peaks on ATAC-seq data

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…

Continue Reading Calling differential peaks on ATAC-seq data

How to get Read Counts from MACS2 output files?

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…

Continue Reading How to get Read Counts from MACS2 output files?

Normalization and differential analysis in ATAC-seq data

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…

Continue Reading Normalization and differential analysis in ATAC-seq data

Bioconductor – MACSdata

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,…

Continue Reading Bioconductor – MACSdata

low number of significant peaks for one contrast

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)….

Continue Reading low number of significant peaks for one contrast

Gene expression profiling of contralateral dorsal root gangl

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…

Continue Reading Gene expression profiling of contralateral dorsal root gangl

Can I use the summits.bed from MACS2 on HOMER

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…

Continue Reading Can I use the summits.bed from MACS2 on HOMER

Using MACS2 parameters

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…

Continue Reading Using MACS2 parameters

How to use IGV (or any genome vis tool) show normalised ChIP-Seq peak intensity?

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…

Continue Reading How to use IGV (or any genome vis tool) show normalised ChIP-Seq peak intensity?

Ubuntu Manpage: macs2_bdgdiff – Ddp 1313.com

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

Continue Reading Ubuntu Manpage: macs2_bdgdiff – Ddp 1313.com

MACS2 BDGDIFF

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

Continue Reading MACS2 BDGDIFF

MACS2 BDGCMP

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

Continue Reading MACS2 BDGCMP

Theuniqueact.com – macs2 bdgdiff for calling differential binding events .

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

Continue Reading Theuniqueact.com – macs2 bdgdiff for calling differential binding events .

Signac CallPeaks from multiple fragment files

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…

Continue Reading Signac CallPeaks from multiple fragment files