Tag: ChiPseq

Remove Uncharacterized chromosomes before alignment in chipseq 0 Hi, I have a question. i am processing a Chipseq experiment on mm10 genome. I did quality check, trimming, alignment, duplicate removal. The “problem” Is that I did not remove Uncharacterized chromosomes from reference fasta genome. I was planning to remove them…

Normalization and Genome-Wide Comparisons with Chipseq 0 Hi all, and apologies if this has been asked before. I have chipseq data (technical and biological replicates for 2 groups) and want to test whether my experimental group has a genome-wide increase in methylation compared to controls. Under the hypothesis, this group…

Multi-factor designs in DiffBind 1 Dears, I’m trying to analyze some ChIPseq data using DiffBind. Samples has been processed in two different times SampleID Name Factor IP Condition Replicates 5 PBS_Pol2 S3 Batch1 Pol2 PBS 1 6 PBS_Pol2 S9 Batch2 Pol2 PBS 2 7 C26_Pol2 S4 Batch1 Pol2 C26 1…

Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…

How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)? 0 I have data from a human ChIP-Seq-like experiment where some samples were treated with a drug in combination with a synthetic plasmid. Now, I’d like to check if the plasmid was incorporated (partial or total) somehow…

deeptools k-means clustering 0 Hello everyone, I have a straightforward query. I generated a heatmap for my ChIP-seq data using deeptools’ plotHeatmap function and applied k-means clustering for analysis. Now, I’m eager to identify the specific peaks associated with each cluster. Can you please guide me on how to obtain…

CHIPSEQ Analysis , DiffBind Parameters 0 Hello, Regarding Diffbind, How does diffbind calculate common peaks with the samples. I’m observing that certain peaks identified as common using bedtools intersect are not appearing in the output report file generated after DiffBind analysis Command used to write the file : res_deseq <-…

Forum:CHIPSEQ : Cut AND Run , DiffBind Parameters 0 Hello I have been using DiffBind to perform differential enrichment analysis on my ChIP-seq Cut and Run dataset where I have 2 sample groups, Control and YY1_overexpression, with 4 replicates in each sample group. (Peak Calling was done through SEACR) 8…

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…

Hi all, I am a newbie in ChIP-seq, and I conducted my analysis using the nfcore ChIPseq pipeline. After reviewing the results, I now need to perform more specific analyses. With nfcore, I generated informative heatmaps that provide a general overview of my ChIP-seq data (I will upload the heatmap)….

UCSC Genome Browser Custom Track Blank 0 Hello, I have a bigwig (.bw) file which I can properly view on IGV. IGV makes it very difficult to edit the figure nicely so I am trying to view it in the UCSC genome browser. I uploaded my data to cyverse and…

Calculation of ChIP-seq normalization factors with non-conventional spike-in assumptions 0 I have an experimental setup where there are known global shifts in levels of our histone mark of interest due to a histone mutation. We include spike-in chromatin in each sample, but we know that the spikein levels are not…

DOI: 10.18129/B9.bioc.DESeq2   This is the development version of DESeq2; for the stable release version, see DESeq2. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: Development (3.19) Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

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…

    This package is for version 2.14 of Bioconductor; for the stable, up-to-date release version, see GenomicRanges. Representation and manipulation of genomic intervals Bioconductor version: 2.14 The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyze high-throughput sequencing…

Hi Lisa, You also need to modify the gtf annotation file using: sed ‘/^#/d’ annotation_file.gtf > annotation_file_no_header.gtf Best, Alex > On 12. Oct 2022, at 15:07, Bora Uyar <borauy…@gmail.com> wrote: > > You would need to check how your fasta headers look and how the chromosomes are represented in…

Got an error when using chilin 0 I installed chilin and all the dependencies following the guidance, but when I run bash foxa1 and my own data, I got an error as below: Traceback (most recent call last): File “/chipseq/3.fastqc/chilin/software/mdseqpos/bin/MDSeqPos.py”, line 421, in <module> main() File “/chipseq/3.fastqc/chilin/software/mdseqpos/bin/MDSeqPos.py”, line 385, in…

DOI: 10.18129/B9.bioc.regioneR   This is the development version of regioneR; for the stable release version, see regioneR. Association analysis of genomic regions based on permutation tests Bioconductor version: Development (3.19) regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other…

        NGS Training Next Generation Sequencing (NGS), a recently evolved technology, have served a lot in the research and development sector of our society. NGS methods are highly parallelized enabling to sequence thousands to millions of molecules simultaneously. This technology results into huge amount of data, which…

DiffBind:Using diffbind with only two replicates per condition 0 I have 6 samples from 3 conditions with two replicates for each condition and I want to make a comparison of these conditions amongst each other. Here is the sample info: SampleID Factor Condtion Replicate PeakCaller 1 Mel239_1 CTCF Mel239 1…

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…

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…

Normalizing Chip seq data using fruit fly genome 0 Hello I have the human chip seq data on which I want to perform the chip seqanalysis. In many papers it has been referred to normalize the data using the spike in method. I have done the alignment of the data…

Hypoxia, the formation of reactive oxygen species (ROS), and subsequent oxidative stress in synovial tissues are key events in the pathogenesis of RA1. We provide here evidence that CBP and p300 are pivotal regulators of the adaptive response of SF that integrate the cell`s transcriptional and functional regulation of stress…

How do mRNASeq, BulkRNASeq, and TotalRNASeq differ in terms of workflow? 0 I want to look for differential gene expression a dataset from a collaborating lab. I have successfully done end-to-end analysis for mRNASeq, CHIPSeq and ATACSeq but I’m very confused about analyzing BulkRNASeq and TotalRNASeq. How different is the…

DOI: 10.18129/B9.bioc.GreyListChIP     This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see GreyListChIP. Grey Lists — Mask Artefact Regions Based on ChIP Inputs Bioconductor version: 3.11 Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during…

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…

Transcription factor co-localization p-values 0 I have ChIPSeq peak data for TF A and TF B in bed format. On examining these in a genome browser together, I see that there are many instances when TFBS for both A and B are close to each other. What kind of statistical…

DOI: 10.18129/B9.bioc.Linnorm   This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Linnorm. Linear model and normality based normalization and transformation method (Linnorm) Bioconductor version: 3.16 Linnorm is an algorithm for normalizing and transforming RNA-seq, single cell RNA-seq, ChIP-seq count data or any large…

Chipseq analysis on repeat genes 0 Hello everyone I am in need of some tips to analyze and make heatmaps as shown in this figure C and G. I already have downloaded the repeatmasker list. I want to compare my chromatin data with repeat elements and see their enrichment. I…

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…

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…

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…

DOI: 10.18129/B9.bioc.CeTF   Coexpression for Transcription Factors using Regulatory Impact Factors and Partial Correlation and Information Theory analysis Bioconductor version: Release (3.17) This package provides the necessary functions for performing the Partial Correlation coefficient with Information Theory (PCIT) (Reverter and Chan 2008) and Regulatory Impact Factors (RIF) (Reverter et al….

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…

DOI: 10.18129/B9.bioc.ChIPsim     Simulation of ChIP-seq experiments Bioconductor version: Release (3.5) A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments. Author: Peter Humburg Maintainer: Peter Humburg <Peter.Humburg at gmail.com> Citation (from within R,…

Bioinformatics Analyst II/III Job ID: req3719Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

DOI: 10.18129/B9.bioc.vulcan     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see vulcan. VirtUaL ChIP-Seq data Analysis using Networks Bioconductor version: 3.15 Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a…

Converting SAM to BAM files 1 What is a simple command that I can use to convert SAM to BAM files without losing any reads info? Thank you! chipseq • 114 views samtools view -o out.bam in.sam Please read the samtools manual for details on pretty much any sam/bam manipulation,…

Extremely high ChIP-seq peak at mouse Chr2 “Gm10800” region 1 I was dealing with some CUT&TAG ChIP-seq data(for TF). After mapping and peak calling, I tried to use IGV to observe their peak distribution around the genome, and I found there are a a great number of peak/reads mapped to…

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…

New mouse reference genome (GRCm39/mm39) 1 Hi, I am planning to perform sequencing alignment using the new mouse reference genome mm39 available on UCSC: hgdownload.soe.ucsc.edu/goldenPath/mm39/bigZips/ (bowtie2 on chipseq data). Did I understand correctly that both mm39.2bit and mm39.fa.gz are the same and I can use either of them (2bit file…

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DOI: 10.18129/B9.bioc.rmspc   Multiple Sample Peak Calling Bioconductor version: Release (3.17) The rmspc package runs MSPC (Multiple Sample Peak Calling) software using R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly known as “peaks”), each indicating a protein-DNA interaction or a specific chromatin modification. When replicate…

GDIT’s Military Health team is seeking a Data Bioinformatics Analyst in support of the Naval Health Research Center (NHRC) Infectious Disease Field Surveillance and Laboratory Research Services. As the Navy hub for the Armed Forces Health Surveillance Center the NHRC Operational Infectious Diseases Directorate conducts on-going, laboratory-based surveillance of US…

Unusual pattern in heatmap from ChIP-seq 0 Hello! I am plotting some heatmaps for a certain histone mark from a ChIP-seq experiment. I am producing the heatmaps using both computeMatrix and plotHeatmap functions from deeptools. The coordinates regions used for computeMatrix are all coding regions for the mouse genome, sorted…

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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…

How to compare peak profiles for a subset of ChIPseq genes 0 Hello, My goal is to compare the peak profiles between WT and MT strains for a subset of genes in a yeast experiment I have completed. Specifically, I would like to: generate a ranked list of the genes…

Job Details Bioinformatics Analyst II/III Job ID: req3605 Employee Type: exempt full-time Division: Bioinformatics and Computational Science Facility: NIH Location: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and…

    This package is for version 2.10 of Bioconductor; for the stable, up-to-date release version, see DESeq. Differential gene expression analysis based on the negative binomial distribution Bioconductor version: 2.10 Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model…

DOI: 10.18129/B9.bioc.chipenrich     This package is for version 3.12 of Bioconductor; for the stable, up-to-date release version, see chipenrich. Gene Set Enrichment For ChIP-seq Peak Data Bioconductor version: 3.12 ChIP-Enrich and Poly-Enrich perform gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for…

COVINA, Calif., July 11, 2023 /PRNewswire/ — According to Prophecy Market Insights “Next-Generation Sequencing Informatics Market accounted for US$ 9.23 billion in 2022 and is estimated to be US$ 35.3 billion by 2032 and is anticipated to register a CAGR of 13.5%” Prophecy_Market_Insights_Logo What is the overview of Next-Generation Sequencing…

DOI: 10.18129/B9.bioc.ChromSCape     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see ChromSCape. Analysis of single-cell epigenomics datasets with a Shiny App Bioconductor version: 3.15 ChromSCape – Chromatin landscape profiling for Single Cells – is a ready-to-launch user-friendly Shiny Application for the analysis…

Job ID: req3312Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USAThe Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc. The lab addresses some…

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…

Bioinformatics Analyst II/III Job ID: req3605Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

How to interpret chipseq profile plot 1 Hello, I am new to chipseq and generated a profile plot during my diffbind analysis. I was hoping someone could help me understand what the bars straight across mean as profile plots online seem to have various signals around for a site instead…

Blacklist for bacterial genome [ChIPseq]? 1 Hi there, I am working on a ChIPseq experiment with bacteria. I have the following questions: 1) Is blacklisting such a small genome necessary for a ChIPseq analysis (4.4 Mbp)? 2) Does ENCODE only provide blacklists for model organisms (mouse, fly, human, worm)? 3)…

DOI: 10.18129/B9.bioc.epigenomix     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see epigenomix. Epigenetic and gene transcription data normalization and integration with mixture models Bioconductor version: 3.13 A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification…

DOI: 10.18129/B9.bioc.iASeq     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see iASeq. iASeq: integrating multiple sequencing datasets for detecting allele-specific events Bioconductor version: 3.13 It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and…

Answer: multiple filters in biomaRt by RuBBiT0 &utrif; 10 First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro… Comment: Diffbind “No genome detected” by kyliecode • 0 Hi Dr. Stark, Thanks very…

DOI: 10.18129/B9.bioc.karyoploteR     This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see karyoploteR. Plot customizable linear genomes displaying arbitrary data Bioconductor version: 3.13 karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them….

Junior Bioinformatics Analyst Job ID: req3312Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc.  The lab addresses some…

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…

Which data should I select in Encode chip-seq data? 1 I want to analyze the ENCODE ChIP-seq data. In this case, which data should I select? I will analyze the peaks from replicate 1 and 2 and detect the common peaks. Should I download the files ‘ENCFF162ADN’ (replicate 1) and…

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,…

Bioinformatics Analyst IV Job ID: req2734Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

use ROSE to identify super enhancer 0 hey everyone, i want to use ROSE to identify super enhancer and to see if there is difference in the super enhancer after some treatment in lung cancer cell line i see that this is the typical use: [user@cn3107 ~]$ ROSE_main.py -h Usage:…

This is the development version of GenomicRanges; for the stable release version, see GenomicRanges. The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing…

Bioinformatics Analyst IV Job ID: req2734Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research, Inc….

DOI: 10.18129/B9.bioc.EDDA     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see EDDA. Experimental…

Job Description: GDIT’s Military Health team is seeking a Data Manager – Bioinformatics Analyst in support of the Naval Health Research Center (NHRC) Infectious Disease Field Surveillance and Laboratory Research Services. As the Navy hub for the Armed Forces Health Surveillance Center the NHRC Operational Infectious Diseases Directorate conducts on-going,…

Infrastructure for Biostrings-based genome data packages Bioconductor version: 2.5 Infrastructure shared by all the Biostrings-based genome data packages Author: Herve Pages Maintainer: H. Pages <hpages at fhcrc.org> To install this package, start R and enter: source(“http://bioconductor.org/biocLite.R”) biocLite(“BSgenome”) To cite this package in a publication, start R and enter: citation(“BSgenome”) Documentation…

Hello, I am have ChIPseq data from histone marks from 2 different condition (mock and treated with 2 biological replicas each) and the aim of my analysis is to study whether a particular histone mark is enriched in one condition versus the other. I am new to bioinformatic and I…

ChIPseq w/ polyploid genome : Xenopus laevis 0 Hello, I have recently undertaken reanalyzing a transcription factor ChIPseq done in Xenopus laevis. I started with the raw data, which includes two replicates for a transcription factor chip, and a DNA input control file. These are all fastq files. After aligning…

samtools idxstats not removing ChrM 2 I am trying to remove ChrM from my ChIP-seq data. Below is my pipeline for one sample up to where I am having the issue (samtools idxstats). The output file from samtools idxstats is the same size as the input so it doesn’t look…

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Bioinformatics Analyst II/III Job ID: req3427Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

Cell culture hTERT-RPE-1 WT and hTERT RPE-1 TP53−/− (46, XX)27 cells were a gift from J. Korbel. The cells were grown in DMEM/F-12, GlutaMAX (10565018) supplemented with 10% FBS (Thermo Fisher Scientific, 10270106) and 1% antibiotic–antimycotic (Thermo Fisher Scientific, 15240062). CP-A (KR-42421) (47, XY) cells were purchased from the American Type…

Chiseq files for deseq2 0 Hello everyone, I have 4 peaks bed files and i want to create count matrix for analysis in deseq2 I want to see the difference acetylation between them, I want in the column the 4 samples, and in the rows peaks I understand i can…

    This package is for version 2.13 of Bioconductor; for the stable, up-to-date release version, see NarrowPeaks. Analysis of Variation in ChIP-seq using Functional PCA Statistics Bioconductor version: 2.13 The double aim of the package is to apply a functional version of principal component analysis (FPCA) to: (1) Process…

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,…

Infrastructure for manipulating intervals on sequences Bioconductor version: 2.6 The package provides efficient low-level and highly reusable S4 classes for storing ranges of integers, RLE vectors (Run-Length Encoding), and, more generally, data that can be organized sequentially, as well as views on these sequences. Efficient list-like classes are also provided…

Hi, I am running the HTSeqGenie on both MacOS and Linux with the test TP53 samples. They both gave me error in reading the fastq files. It seems having problems reading the fastq.gz files in each parallel process. Could anyone help me with this please? Error are at below: checkConfig.R/checkConfig.template:…

Bioinformatics Analyst IV Job ID: req3398Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…

I am trying to index my reference genome using bwa-mem2 (latest version). I downloaded GRCm39.primary_assembly.genome.fa from www.gencodegenes.org/mouse/release_M27.html and run the following bwa-mem2-2.0pre2_x64-linux/bwa-mem2 index /media/jay/Data/reference_genome/GRCm39.primary_assembly.genome.fa I got this output [bwa_index] Pack FASTA… 7.03 sec init ticks = 216871092051 ref seq len = 5456444902 binary seq ticks = 176853625961 build index ticks…

Suppose I’m looking at a GEO entry like so: www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM946533 Notice at the bottom is a table of ‘Supplementary files’, containing broadpeak and bigwig files. I’m wondering how to download these using Entrez. I’ve tried a variety of approaches, the “closest” I’ve gotten is the following: esearch -db gds -query…

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…

DOI: 10.18129/B9.bioc.MIRA     Methylation-Based Inference of Regulatory Activity Bioconductor version: Release (3.15) DNA methylation contains information about the regulatory state of the cell. MIRA aggregates genome-scale DNA methylation data into a DNA methylation profile for a given region set with shared biological annotation. Using this profile, MIRA infers and…

DOI: 10.18129/B9.bioc.gcapc     GC Aware Peak Caller Bioconductor version: Release (3.13) Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation. Author: Mingxiang Teng and…

DOI: 10.18129/B9.bioc.metaseqR2     An R package for the analysis and result reporting of RNA-Seq data by combining multiple statistical algorithms Bioconductor version: Release (3.11) Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining…

DOI: 10.18129/B9.bioc.DiffBind     This package is for version 3.15 of Bioconductor; for the stable, up-to-date release version, see DiffBind. Differential Binding Analysis of ChIP-Seq Peak Data Bioconductor version: 3.15 Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions….

Choose the correct answer: 1. Which method should you use to identify novel targets of a selected RNA binding protein (Select all that apply). A. ChIPseq B. ATACseq C. CLIP 2. Mark all the alternative splicing events (Select all that apply). A. exon skipping B. alternative polyadenylation C. alternative promoter…

DOI: 10.18129/B9.bioc.samExploreR     This package is deprecated. It will probably be removed from Bioconductor. Please refer to the package end-of-life guidelines for more information. This package is for version 3.13 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see samExploreR. samExploreR…

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    This package is for version 3.2 of Bioconductor; for the stable, up-to-date release version, see MEDIPS. DNA IP-seq data analysis Bioconductor version: 3.2 MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of…

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?…

Junior Bioinformatics Analyst Job ID: req3312Employee Type: exempt full-timeDivision: Bioinformatics and Computational ScienceFacility: NIHLocation: NIH Campus 9000 Rockville Pike, Bethesda, MD 20892 USA The Frederick National Laboratory is a Federally Funded Research and Development Center (FFRDC) sponsored by the National Cancer Institute (NCI) and operated by Leidos Biomedical Research,…