Tag: bigWig

Cell culture Cell lines (MDA-MB-231, 4T1 and RPE-1) were purchased from the American Type Culture Collection (ATCC). TP53-knockout MCF10A, TP53-knockout RPE-1 and Trex1 knockout 4T1 cells were gifts from the Maciejowski laboratory at the Memorial Sloan Kettering Cancer Center (MSKCC). OVCAR-3 cells were a gift from J. D. Gonzales. All…

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…

Litman, G. W., Cannon, J. P. & Dishaw, L. J. Reconstructing immune phylogeny: New perspectives. Nat. Rev. Immunol. 5, 866–879 (2005). Article  CAS  PubMed  PubMed Central  Google Scholar  Criscitiello, M. F. & de Figueiredo, P. Fifty shades of immune defense. Heitman J, editor. PLoS Pathog. 9, e1003110 (2013). Article  CAS …

I am trying to get computeMatrix for bigwig file in specific genomic region using deeptools.Below is the code I am using computeMatrix reference-point –referencePoint TSS \ -b 1000 -a 1000 \ -R ~/Desktop/ATAC/ATAC/Inducible_elements_Greenberg.bed \ -S ~/Desktop/ATAC/Control.mRp.clN.bigWig \ –skipZeros \ -o ~/Desktop/ATAC/matrix_controlmRPATACBasalcomputematrix.gz \ But I get the following error File “/Library/Frameworks/Python.framework/Versions/3.11/lib/python3.11/site-packages/numpy/__init__.py”,…

Average bigwig files (not sum) 1 Hello, I have bigwig (RPKM) files of a chip-seq experiment for treatment and control conditions which I am trying to compare. I have 3 replicates for control and 5 replicates for treatment condition. To show the average difference in signal, I merged the replicates…

GRange: Average Metadata Value from 3 Replicates 1 I have CPM-normalized genome coverage data from three replicate experiments in the form of bigwig files. I read these into R using rtracklayer and now have 3 GRange objects. For each basepair, I want to calculate the mean score of the three…

scEC&T sequencing A detailed, step-by-step protocol of scEC&T-seq is available on the Nature Protocol Exchange46 and is described below. The duration of the protocol is approximately 8 days per 96-well plate. Cell culture Human tumor cell lines were obtained from ATCC (CHP-212) or were provided by J. J. Molenaar (TR14; Princess…

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…

Article describing tool (for citations): O. Tange (2011): GNU Parallel – The Command-Line Power Tool, ;login: The USENIX Magazine, February 2011:42-47. Author’s website for obtaining code: www.gnu.org/software/parallel/ All new computers have multiple cores. Many bioinformatics tools are serial in nature and will therefore not use the multiple cores. However, many…

Error: unrecognized arguments using deepTools bamCoverage 0 Hello everyone! I`m trying to visualize ChIP-seq data with deepTools but facing errors when use optional arguments for normalization. Comands like: bamCoverage -b file.bam -o file.bigWig -of bigwig –normalizeUsing RPGC –effectiveGenomeSize 2862010578 –ignoreForNormalization chrX chrY bamCompare -b1 file-1.bam -b2 file-2.bam -o files-1-2.bigWig -of…

Ethics statement All animal experimentation was conducted according to the National Institutes of Health guidelines for the housing and care of laboratory animals. All experiments were performed in accordance with institutional regulations after review and approval by the Animal Studies Committee at Washington University School of Medicine in St Louis,…

ATAC: Finding peaks in BW file 0 I’m trying to analyze this ATAC dataset. Does anyone know if the bw files in the supplementary data the peaks themselves, or do I need to process them further to get the peaks? I opened one of them using import.bw from rtracklayer, and…

Bristol-Myers Squibb BMY has recently been enjoying a string of positive regulatory updates. The company’s psoriasis drug Sotyktu (deucravacitinib) recently got approved by the European Commission (EC). Sotyktu is a first-in-class, selective tyrosine kinase 2 (TYK2) inhibitor for treating adults with moderate-to-severe plaque psoriasis who are candidates for systemic therapy,…

Does the bigwig file of a single-end chip-seq shows 2 peaks for a fragment whereas the paired-end show one peak ? 0 My thinking goes like this. In a single-end chip-seq, there will be accumulation of reads in either side of any putative fragment of DNA so I feel the…

Any straightforward way to re-bin a bigWig file? 0 I was wondering if anyone has come across a tool that can take a bigwig file and a binsize as inputs, and get a bigwig with a new bin size as output? Like say I have sample.bw with a binsize of…

Which ATAC-seq SAM/BAM fields are required for bigwig generation by deeptools bamCoverage? 0 Hi, I plan to convert SAM file into BED file using bedops sam2bed tool and perform “chr start and end coordinates” data points manipulation to break di-nucleosome and tri-nucleosome data points into mono-nucleosome data points, then convert…

Via a couple Kent tools and BEDOPS, convert the bigWig file to sorted BED: $ bigWigToBedGraph input.bw input.bedgraph $ awk ‘{ print $1″\t”$2″\t”$3″\tid-“NR”\t”$4; }’ input.bedgraph | sort-bed – > input.bed Get the chromosomal bounds for your genome build of interest, e.g. hg19, and convert them into sorted BED: $ fetchChromSizes…

Deeptools clustering differs when clustering sample as standalone and together with other samples 0 Hi! I am using deepTools to generate heatmaps for different serine phosphorilations (ser2, ser5, ser7).I have observed a behavior that I don’t understand or I can’t explain, so maybe you could help me with it.I am…

I generated summit.bed files from my experiment cut&run, and I followed the below steps to get and visualize the bigwig files. 1) I used awk to get a bedgraph: awk ‘{printf “%s\t%d\t%d\t%2.3f\n” , $1,$2,$3,$5}’ myBed.bed > myFile.bedgraph 2) Sorting the bed files: sort -k1,1 -k2,2n myFile.bedgraph > myFile_sorted.bedgraph 3) Chrom.size:…

I’m trying to bin 1x normalized ATAC-seq bigWig (generated by the bamCoverage function) with the multiBigwigSummary function in deepTools with the intention of clustering several ATAC-seq samples with deepTool’s plotCorrelation function. My bamCoverage commands look like this: > bamCoverage -b input.bam -o output.SeqDepthNorm.bw -p “max” –effectiveGenomeSize 2805636331 –normalizeUsing RPGC -ignore…

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…

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…

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…

Cell culture Normal Human Melanocytes (NHM) were cultured in Dermal Cell Basal Medium (ATCC) with the addition of 5 µg/ml Insulin, 50 µg/ml Ascorbic Acid, 6 mM L-Glutamine, 1.0 µM Epinephrine, 1.5 mM Calcium Chloride, Peptide Growth Factor and M8 Supplement. Dermal fibroblasts (DFs) were isolated from neonatal mice and iPS reprogramming was performed as…

making a BIGWIG from BAM file 1 Hello everyone, I have 50 BAM files, some of them single-end and some of them paired-end. Well, I want to make a single bigwig file by combining reads from all of these bam files. For this, I merged all bam files to a…

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…

bamComparing ChIp-Seq samples with strange coverage between chipped and Input 0 I’m having some troubles both estimating the quality and understanding the results of my ChIp-Seq samples as well as to decide how to continue. I hope I can find some help/advice here. I have three conditions, each with duplicates…

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…

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…

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…

Visualizing Chip Peak files from ENCODE 1 Hello. I am trying to view chip peak files in the WashU genome browser from Encode. Specifically I am needing to visualize the peak files for the following: ENCFF017XLW, ENCFF188SZS, and ENCFF367KIF These files are in BED format and I have found a…

BedGraph to bigWig 0 Hi, I am using Galaxy to convert BedGraph to bigWig using Wig/BedGraph-to-bigWig . However, it doesn’t begin to execute even though its been an hour nor it gives me any error. Can someone please help? Thank you! ATACseq bigWig BedGraph Galaxy • 172 views Login before…

Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…

Bedtools Bam To Bed With Code Examples With this article, we’ll look at some examples of how to address the Bedtools Bam To Bed problem . bedtools bamtobed [OPTIONS] -i <BAM> As we have seen, a large number of examples were utilised in order to solve the Bedtools Bam To…

Although the hypothesis of gene-regulatory network (GRN) cooption is a plausible model to explain the origin of morphological novelties (1), there has been limited empirical evidence to show that this mechanism led to the origin of any novel trait. Several hypotheses have been proposed for the origin of butterfly eyespots,…

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…

‘Negative’ and ‘Positive’ bigWig RNAseq files: how to deal with these??? 0 @bas_work-22458 Last seen 1 day ago Netherlands Hi: Before diving into analysis of (public) RNAseq data, I discovered that the data are stored in two BigWig files per sample (i.e. carrying a ‘neg’ identifier, the other a ‘pos’…

computeMatrix in deeptool is Running with no result 0 Hi All, I wonder if someone can help me in explaining what to input on the -R <bed file> argument of the code below? computeMatrix scale-regions -S <bigwig file(s)> -R <bed file> -b 1000 what I did for example, I download…

Deeptools: computeMatrix can’t read file 1 Hi, I generated bigwig file using bamCoverage with the following code. bamCoverage -b A.bam -o A.bw –binSize 10 -p max –normalizeUsing CPM Then, I tried to use computeMatrix computeMatrix -S A.bw -R B.bw -o C but I got the following error usage: computeMatrix [-h]…

What is the relationship between the value of the bigwig file generated by MACS2 and the read count? 0 What is the relationship between the value of the bigwig file generated by MACS2 and the read count? When using Deseq2 or edgeR to identify the differential peak, because the value…

Gene Expression Prediction from DNA sequences 1 Hi everyone! I am a university student working on my Master’s thesis. I worked on a paper called Xpresso which has the purpose to predict the gene expression levels starting from DNA sequences using deep learning techniques. Now, my lecturers have asked me…

How to identify differential enhancers? 0 Deseq2 or edgeR only allow the input of reads count to identify differential regions, but I get less differential enhancer with reads count, can I use the signal from the bigwig file as input to deseq2 or edgeR to identify the differential enhancer? EdgeR…

Greetings, I hope everyone is doing well. So I used computeMatrix from deeptools to calculate the coverage of certain samples. The bigwig signal is in BPM (generated by bamCoverage). I want to transform the values in the matrix to a log2 scale to get the enrichment profile or heatmap in…

We are using the package ‘rtracklayer’ to load and manipulate bigwig files as part of a larger script. We need to access bigwig files from an http-server, and we can do this smoothly on MacOS, but we can’t get it to work on Windows machines – while local bigwig files…

MultiBigwigSummary of deepTools keeps on running for a long time 1 I am trying to generate a merged bigwig file using multiBigwigSummary for using in the plotCorrelation tool in deepTools. However, the 8 files are running in this program for almost 5hours. How long does it usually take to generate…

Human research participants We have complied with all relevant ethical regulations and informed consent was obtained from all participants. This work was approved by the Cornell University IRB under protocol 1506005662. Animal research This work was approved by the Cornell University IACUC under protocol 2009-0044. Welfare and handling of all…

Reads detected/”spill over” on introns after using bamCoverage function from deepTools 0 Hello! We recently used the recent version of bamCoverage from the deepTools suite for our ribo-seq and RNA-seq bam files to generate bigwig files. The conversions ran smoothly, however when we loaded the bigwig files into IGV, we…

ChIP-seq heatmap input bed file 0 Hello, I am getting confused about the ChIP-seq heatmap concept. In particular, what should be the .bed file exactly? For example while using deeptools before plotHeatmap, computeMatrix is used and you should provide bigwig file and a bed file. Bigwig file should be the…

Home Bioconductor 3.14 Released October 27, 2021 Bioconductors: We are pleased to announce Bioconductor 3.14, consisting of 2083 software packages, 408 experiment data packages, 904 annotation packages, 29 workflows and 8 books. There are 89 new software packages, 13 new data experiment packages, 10 new annotation packages, 1 new workflow,…

Hi, I have a question about whether I should set the sizeFactors to 1 prior to using DESeq2 on the counts obtained from derfinder. I have normalized bigwig files ( using deepTools ), which I use as input to derfinder. Following the instructions in the users guide : lcolladotor.github.io/derfinder/articles/derfinder-users-guide.html#expressed-regions-level-1 My…

Measure genome-wide agreement of peaks in 0 Is there an approach to measure agreement in epigenomic signals e.g. histone marks (continuous -log10 p-vals after peak calling)? This approach should also work across assays or cell types. For example, how similar is the DNAse-seq signal across Neutrophils, Monocytes and T-cells? Are…

Asked by: Vada Ratke Score: 4.7/5 (25 votes) BigWig is a file format for display of dense, continuous data in a genome browser track, created by conversion from Wiggle (WIG) format. BigWig format is described at the UCSC Genome Bioinformatics web site, and the Broad Institute file format guide provides…

Statistics and reproducibility For multiplex fluorescent in situ hybridization (FISH) and immunofluorescence staining experiments, each ISH probe combination was repeated with similar results on at least two separate individuals per species, and on at least two sections per individual. The experiments were not randomized and the investigators were not blinded…

What you describe seems to be a difference in signal-to-noise ratio which is not uncommon. This is where more elaborate normalization methods such as TMM from edgeR or RLE from DESeq2 come into play. See the following links on why these methods are superior. The videos talk about RNA-seq but…

Forum:Misuse of RPKM or TPM normalization when comparing across samples and sequencing protocols 2 Published in the RNA Journal in 2020 – this paper argues that if the original RNA amount in the different samples is different, TPM should not be used to find differentially expressed genes. www.ncbi.nlm.nih.gov/pmc/articles/PMC7373998/ Seems like…

Create combined CpG and non-CpG bedgraphs for DNA methylation using Bismark 0 Hello, previously, I was using Bismark with the ‘–comprehensive’ option to generate the individual bedgraph files from which we made the bigWigs. For one particular figure, my boss wants me to generate merged bdg files so that we…

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…

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…

Where can I get ?or how can I make a mappability track for hg38 assembly 2 Lucky you @manojmumar_bhosale I worked on similar problem recently and therefore have the bash script you can use. Required tools: GEM libary from here UCSC’s wigToBigWig from here (I chose binary for Linux 64…

convert genomic bigWig file to transcriptome space 0 Hi all, Is anyone aware of a function to convert a bw file mapped to a genome to map to a transcriptome (of said genome), where the input would be the genomic bw file and gff/gtf/bed annotation and output a single ‘transcriptomic’…

Get chromosome names of a bigwig file 1 I would like to extract the chromosome names from a bigwig (.bw) file. Is there an existing tool/command? (I need to verify they match the genome annotation file I am working with + diagnose failing multiBigwigSummary) bigwig • 37 views • link…

Download bigWig files of publicly available ChIP-seq samples 1 There are a couple of efforts to provide quality controls of publicly available ChIP-seq data sets (e.g. www.ngs-qc.org/ and CISTROME. But is there a way to obtain the normalized bigWig files? Cistrome, for example, allows you to explore the coverage data…

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…

STAR split reads into two strands 0 Hi all, I’m trying to find a way to split reads mapped with STAR into two separate bam-files, one for each strand. STAR is able to do that when creating bedgraph or bigwig outputs (–outWigType and –outWigStrand), however I can not find any…

bedGraph chrom.sizes myBigWig.bw (Note that the bedGraphToBigWig program DOES NOT accept a gzipped bedGraph input file.) Move the newly … Source link

Convert Sam To Bigwig Convert BAM into bigwig for chicken Hi, I used functions of “Create a BedGraph of genome coverage” and “Wig/BedGraph-to- … Source link

It is too easy to make error report in the bedGraphToBigWig process. I want to save the time for the fresh people. The following procedure would be work well for majority situations.  1, bedGraph should be without header before sorting awk ‘NR!=1’ input.bedGraph > input.deheader.bedGraph 2, bedGraph should be sorted sort…