Tag: ChiPseq

Split merged Bam file without replacement

Split merged Bam file without replacement 0 Hi guys, I have 5 bam (ChIPseq PE data sorted by position) files that came from 5 different murine cortexes (mice that belong to the same group, so biological replicates), however I have a lot of group variability. I’m thinking to merge all…

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Bioconductor – Rsubread

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see Rsubread. Rsubread: high-performance read alignment, quantification and mutation discovery Bioconductor version: 2.13 This R package provides easy-to-use tools for analyzing next-gen sequencing read data. Functions of these tools include quality assessment, read alignment,…

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ChIPseq annotation with replicates

ChIPseq annotation with replicates 0 Hi, What’s the best way to annotate chip peaks in case of replicates? I have 3 replicates each group. I understand Chipseeker is a very convenient tool, but I can’t find a clear example of how to merge replicates and annotate the peaks for visualization?…

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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…

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Bioconductor – derfinder (development version)

DOI: 10.18129/B9.bioc.derfinder     This is the development version of derfinder; for the stable release version, see derfinder. Annotation-agnostic differential expression analysis of RNA-seq data at base-pair resolution via the DER Finder approach Bioconductor version: Development (3.15) This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two…

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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  …

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Bioconductor – ChIPQC

    This package is for version 3.1 of Bioconductor; for the stable, up-to-date release version, see ChIPQC. Quality metrics for ChIPseq data Bioconductor version: 3.1 Quality metrics for ChIPseq data Author: Tom Carroll, Wei Liu, Ines de Santiago, Rory Stark Maintainer: Tom Carroll <tc.infomatics at gmail.com>, Rory Stark <rory.stark…

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NIH-SOAR-NCI-Bioinformatics Scientist in Rockville, MD

Axle Informatics is a bioscience and information technology company that offers advancements in translational research, biomedical informatics, and data science applications to research centers and healthcare organizations around the globe. With experts in biomedical science, software engineering, and program management, we focus on developing and applying research tools and techniques…

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ChIP-Seq density plot between two groups of genes

ChIP-Seq density plot between two groups of genes 1 Hello I have Chipseq data(.bam file) from this I have normalized my bam file BPM method and created the density plot using deeptools, density plot i have created for two group of genes (Genes of interest) group of genes are different…

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Chipseq density plot between two grops of genes

Chipseq density plot between two grops of genes 1 Hello I have Chipseq data(.bam file) from this I have normalized my bam file BPM method and created the density plot using deeptools, density plot i have created for two group of genes (Genes of interest) group of genes are different…

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Removing contamination with SNP tools

Removing contamination with SNP tools 0 Hello everyone, Currently, I’m working on a ChIPseq dataset where I will analyze chromatin marks on transposons and genes in a fungus. Unfortunately, I got some contamination in my data from a closely related species. Because they are so similar, removing contamination based on…

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Bioconductor – csaw

    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see csaw. ChIP-seq analysis with windows Bioconductor version: 3.2 Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control. Author: Aaron Lun <alun at wehi.edu.au>,…

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Bioconductor – ALDEx2

DOI: 10.18129/B9.bioc.ALDEx2     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ALDEx2. Analysis Of Differential Abundance Taking Sample Variation Into Account Bioconductor version: 3.9 A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard…

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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…

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not primary alignment flag filtering does not work

not primary alignment flag filtering does not work 1 Hello, I have a bowtie2 result looking like this; 27823422 reads; of these: 27823422 (100.00%) were unpaired; of these: 2464773 (8.86%) aligned 0 times 19083986 (68.59%) aligned exactly 1 time 6274663 (22.55%) aligned >1 times 91.14% overall alignment rate I am…

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Bioconductor – ChIPComp

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see ChIPComp. Quantitative comparison of multiple ChIP-seq datasets Bioconductor version: 3.4 ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control. Author: Hao Wu, Li Chen, Zhaohui S.Qin, Chi Wang Maintainer:…

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Rockefeller Disability Jobs – Director of Research Bioinformatics in New York, New York, United States

Job: IRC26893 Description Job Title Director of Research Bioinformatics Laboratory / Department Hospital Department Description The Rockefeller University Hospital is funded by the National Institutes of Health and has 20 patient beds for clinical research. The Hospital provides researchers with an opportunity to conduct clinical studies, and offers both normal…

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Bioconductor – chipseq

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see chipseq. chipseq: A package for analyzing chipseq data Bioconductor version: 3.4 Tools for helping process short read data for chipseq experiments Author: Deepayan Sarkar, Robert Gentleman, Michael Lawrence, Zizhen Yao Maintainer: Bioconductor Package…

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dba.count reduces binding matrix, why?

dba.count reduces binding matrix, why? 0 db <- dba(samplesheet) This gives me: db 9 Samples, 138044 sites in matrix (193226 total) then I do db.cnt <- dba.count(db) db.cnt 9 Samples, 55893 sites in matrix I wonder why dba.count is removing more than half of the intervals? diffbind atacseq chipseq diffbind3…

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Bioconductor – MotIV

    This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see MotIV. Motif Identification and Validation Bioconductor version: 3.4 This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize…

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ChIP-seq peak number so high

ChIP-seq peak number so high 0 Hello everyone, I want to ask a general question and your valuable comments about my approach. I am analyzing different ChIP-seq samples from different datasets under same conditions (i.e. : mcf7 er alpha control chip-seq under the same conditions). Some of them have really…

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BIOINFORMATICS SCIENTIST job in in Dubai United Arab Emirates

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

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Bioconductor – systemPipeRdata

DOI: 10.18129/B9.bioc.systemPipeRdata     This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see systemPipeRdata. systemPipeRdata: NGS workflow templates and sample data Bioconductor version: 3.9 systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used…

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merge chipseq peaks with bedtools/other tool

# this should do it, concatenate peak locations in all peaks, sort them and merge cat A B C …. | sort -k1,1 -k2,2n | mergeBed -i stdin > locations.bed To know which files the peaks co-ordinates are merged from, you need to have an identifier in each file before…

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Bowtie2 alignment error with different amount of reads in R1 and R2

Bowtie2 alignment error with different amount of reads in R1 and R2 0 Hi all, I have an issue when trying to align a ChIPseq input reads to the genome using bowtie2. The error that comes up is: Error, fewer reads in file specified with -2 Error, fewer reads in…

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How to proceed with multiple runs ChIP-seq

How to proceed with multiple runs ChIP-seq 0 Hello dear people, I want to ask a question about multiple runs. I want to use this sample; Foxa1 ChIP-seq but it has (also the input) multiple runs: 3 runs I am not sure if I merge them and analyze them as…

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Biocept, Inc. hiring Bioinformatics Scientist in San Diego, California, United States

Tasks and Responsibilities Develop and maintain analysis pipelines for next generation sequencing data. Deep dive analysis of targeted and UMI… Required Skills & Experience MS/PhD in bioinformatics, mathematics, computer science, biology, chemistry, or similar, with 3+ years experience in an industrial environment. Experience in clinical diagnostics desired but not required…

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Bioconductor – marr

DOI: 10.18129/B9.bioc.marr     Maximum rank reproducibility Bioconductor version: Release (3.13) marr (Maximum Rank Reproducibility) is a nonparametric approach that detects reproducible signals using a maximal rank statistic for high-dimensional biological data. In this R package, we implement functions that measures the reproducibility of features per sample pair and sample…

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Cedars-Sinai hiring Research Bioinformatician II – Knott Lab – Bioinformatics & Functional Genomics in Los Angeles, California, United States

The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II!This position provides excellent opportunities for continued scientific development and contributions at the interface between research and clinical translation in dynamic laboratory environments. At the Knott laboratory,…

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Research Bioinformatician II – Knott Lab

Research Bioinformatician II – Knott Lab – Bioinformatics & Functional Genomics Apply Now Share Requisition # HRC0654414 The Knott Laboratory at Cedars-Sinai Medical Center is seeking to hire a highly motivated computational scientist to fill the position of Research Bioinformatician II! This position provides excellent…

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Bioconductor – PICS

DOI: 10.18129/B9.bioc.PICS     Probabilistic inference of ChIP-seq Bioconductor version: Release (3.5) Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach. Author: Xuekui Zhang <xzhang at stat.ubc.ca>, Raphael Gottardo <rgottard at fhcrc.org> Maintainer: Renan Sauteraud <rsautera at fhcrc.org> Citation (from within R, enter citation(“PICS”)): Installation To install this…

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Bioconductor – DESeq2

DOI: 10.18129/B9.bioc.DESeq2     This package is for version 3.10 of Bioconductor; for the stable, up-to-date release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 3.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on…

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Bioinformatics Scientist/Senior Scientist – Torre

Arcus Biosciences is an exciting young company founded on the vision of creating new cancer therapeutics through the utilization of unexploited insights in immunology. The company was formed in 2015 by a group of seasoned researchers from the biotechnology and pharmaceutical industries. We are located in the San Francisco bay…

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Oklahoma Medical Research Foundation hiring Bioinformatics Trainer / Analyst in Oklahoma City, Oklahoma, United States

Competitive salaries and full benefits including, medical, dental, and vision insurance, retirement program, vacation and sick leave, onsite cafe and much more! The Oklahoma Medical Research Foundation (OMRF) is an independent, not-for-profit, biomedical research institute adjacent to the campus of the University of Oklahoma Health Sciences Center (OUHSC) located in…

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Chipseq visualization how to draw the figure

Chipseq visualization how to draw the figure 1 Dose anybody know how to draw the figure using Chpseq data? Any guidance would be appreciated ! (the figure is from The Histone Lysine Demethylase JMJD3/KDM6B Is Recruited to p53 Bound Promoters and Enhancer Elements in a p53 Dependent Manner) peaks Chipseq…

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