Tag: bigWig

DOI: 10.18129/B9.bioc.genomation     Summary, annotation and visualization of genomic data Bioconductor version: Release (3.6) A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome…

Enrichment profiles from counts 0 Hello everyone, I’m currently working with single-cell DamID datasets, focusing on studying protein-DNA interactions. In my dataset for each cell, I have aligned BAM files, counts files in HDF5 format, and count files binned at 100kb intervals. These count files contain the number of unique…

Nucleus preparation from frozen brain tissue for Chromium single-cell multiome ATAC and gene expression analysis M1 tissue was obtained from three human donors (male, aged 42, 29 and 58 years), three macaque donors (male, aged 6 (Macaca mulatta), 6 (M. mulatta) and 14 (Macaca fascicularis) years), three marmoset (Callithrix jacchus)…

Tissue preparation and nucleus isolation All experimental procedures using live animals were approved by the SALK Institute Animal Care and Use Committee under protocol number 18-00006. Adult C57BL/6J male mice were purchased from Jackson Laboratories. Brains were extracted from 56–63-day-old mice and sectioned into 600 µm coronal sections along the anterior–posterior…

Cohorts Saliva and/or blood samples were collected from consenting individuals among four NCIG-partnered communities: Tiwi Islands (comprising the Wurrumiyanga, Pirlangimpi and Millikapiti communities), Galiwin’ku, Titjikala and Yarrabah, between 2015 and 2019. Non-Indigenous comparison data, generated from unrelated Australian individuals of European ancestry, was drawn from two existing biomedical research cohorts:…

Merge two bigwig(+/- strand) files from RNA-seq 2 Hi all, I am working on expression data from EpigeneticRoadmap and wanted to generate an expression track.(Link here) Since the cell line expression data only has bigwig file in two separate files. One from positive strand; the other from negative strand and…

Kahn, S. E., Hull, R. L. & Utzschneider, K. M. Mechanisms linking obesity to insulin resistance and type 2 diabetes. Nature 444, 840–846 (2006). Article  ADS  PubMed  Google Scholar  Halban, P. A. et al. β-cell failure in type 2 diabetes: postulated mechanisms and prospects for prevention and treatment. Diabetes Care…

De novo assembly and repeat-masking To maximize the species diversity of primates in our analyses, we newly sequenced and assembled the genomes of 187 different primate species, initially presented in refs. 11,23, for which no other reference genome assembly was available. In brief, each individual was sequenced with 150 bp paired…

Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…

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…

Adrian1 November 12, 2023, 10:30pm 1 tool: bedgraph-to-bigwig input: bedgraph files from MACS2 output problem: result bigwig file has 0 lines tool standard output: hashMustFindVal: ‘GL456210.1’ not foundtool standard error” grep: write error: Broken pipe Error running wigToBigWig. more details: I used mm39 as the database/build for all my inputs,…

DOI: 10.18129/B9.bioc.rtracklayer     R interface to genome annotation files and the UCSC genome browser Bioconductor version: Release (3.6) Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may…

IGV not showing bigwig track information 0 Hi there, I’m struggling to view some .bw files in IGV – however when I load .bam files into IGV (the same ones used to create the aforementioned .bw files) I do not encounter this issue. Whether I have fundamentally misunderstood what a…

Statistical methods Statistical tests, test statistics and P values are indicated where appropriate in the main text. Categorical associations were established using the chi-squared test of independence if n > 5 for all categories and Fisherʼs exact test otherwise. For both tests, the Python package scipy.stats v1.5.3 implementation was used64. Multiple hypothesis corrections…

BAC plasmids Human (CH17-203N23, CH17-449P15 and CH17-339H2) and mouse (RP23-51O13, RP23-75P20 and RP23-204E8) BACs were purchased from BACPAC Resources Center. Yeast–bacterium shuttle vector pLM1050 was modified by L. Mitchell based on a previous study28. pWZ699 was constructed by inserting a cassette containing pPGK-ΔTK-SV40pA transcription unit and the Actb gene into…

DOI: 10.18129/B9.bioc.megadepth   This is the development version of megadepth; for the stable release version, see megadepth. megadepth: BigWig and BAM related utilities Bioconductor version: Development (3.19) This package provides an R interface to Megadepth by Christopher Wilks available at github.com/ChristopherWilks/megadepth. It is particularly useful for computing the coverage of…

BrdU analysis of yeast replication 0 Hi all, I would like to ask how people normalise their data of BrdU-IP sequencing? This is a plot of BrdU-IP-seq across a region in chromosome V in yeast. BrdU labels nascent DNA so here I am basically seeing newly replicated DNA as the…

Animal models Animal studies were approved by the Institutional Animal Care Use Committee of the Institute of Biosciences and Technology, Texas A&M University (AUP 2020-0195). Most mouse strains bear a C57BL/6 genetic background unless otherwise noted. All the animals were housed in a certified animal facility with a standard dark/light…

Home Bioconductor 3.18 Released October 25, 2023 Bioconductors: We are pleased to announce Bioconductor 3.18, consisting of 2266 software packages, 429 experiment data packages, 920 annotation packages, 30 workflows and 4 books. There are 69 new software packages, 10 new data experiment packages, 8 new annotation packages, no new workflows,…

Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…

Cell culture and treatments Human embryonic lung MRC5 fibroblasts (ATCC) and IMR90 fibroblasts (ATCC) were grown in Dulbecco’s modified Eagle’s medium (Sigma-Aldrich, D5796) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 100 U ml−1 penicillin, 100 μg ml−1 streptomycin and 2 mM l-glutamine and maintained at 37 °C under 5% CO2. MRC5 fibroblasts were cultured in…

How to import bigwig files into igvR 0 Hi, I have aligned RNAseq data as *.bigwig I am trying to import these bigwig files into igvR but I do not know how. I am reading through the docs but I am confused. Can somebody share a line of code and…

ATAC-seq +4 -5 shift 3 Dear all, I saw having the mapped reads have +4 and -5 shift in ATAC-seq is a common practice. Some place says “reads should be shifted + 4 bp and − 5 bp for positive and negative strand respectively, to account for the 9-bp duplication created by DNA repair…

ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…

Yeast strain and growth conditions S. cerevisiae strain BY4741 was grown in YPD media at 30 °C. Saturated cultures were diluted into 300 ml YPD medium with an optical density at 660 nm (OD660) of approximately 0.1 and then grown at 30°C with shaking at 250 rpm until mid-log phase with an OD660 of…

I have a somewhat complicated pipeline in which bam files are converted from bam > bed > bedGraph > bigwig. The final bigwig files are missing genome ranges that have a coverage value of 0, despite a chromosome size file, S288C_R64.fa.fai, being referenced during file type conversion. The missing genome…

htseq-count reports count values for deleted genes 0 I am using htseq-count on BAM files from a bacterial species. We are comparing WT strains as well as two strains with genes knocked out. The knockouts have been verified with whole genome sequencing, but do retain the first 15 and last…

Calling large domains of signal enrichment (broad peaks) from log2,input normalized ChIP-seq data 1 As in the title, I am looking for approaches for calling large heterochromatin domains (like Lamina-associated domains, average size ~200Mb). I would like to start from bigwig files that show the log2(IP library in CPM/input library…

computeMatrix error: [pyBwOpen] bw is NULL! 0 Hi all, I am trying to run computeMatrix in DeepTools and getting the following error: [bwHdrRead] There was an error while reading in the header! [pyBwOpen] bw is NULL! Traceback (most recent call last): File “/Users/bp/opt/anaconda3/bin/computeMatrix”, line 8, in <module> sys.exit(main()) File “/Users/bp/opt/anaconda3/lib/python3.9/site-packages/deeptools/computeMatrix.py”,…

ChIP-seq visualization: Is it valid to do a coverage normalization in addition to applying a spike-in-derived scaling factor? 0 Let’s say a ChIP-seq sample is scaled in the following way: Calculate the percent spike-in reads in the immunoprecipitate (IP) Calculate the percent spike-in reads in the input Calculate the scaling…

Clinical samples and plasma preparation Blood samples from control individuals and patients with multiple myeloma, liver cancer, and lung cancer were obtained from Oregon Health and Science University (OHSU) by Knight Cancer Institute Biolibrary and Oregon Clinical and Translational Research Institute (OCTRI). All samples were collected under OHSU institutional review…

BedGraph to bigwig inside Pipe? 0 Are there any options for converting bedGraph files to bigwig? I have a multi-step pipe that takes a bam file, does several operations in a pipe, and currently outputs a bedGraph file. The only option I know of to get from a bed/bedGraph is…

How to convert BigWig file to GCT File? 0 I have this bigwig file generated from RNA Seq analysis and I want to convert that file into GCT file. How can I convert that? Is there any n number of steps or can I do it directly using any tool…

Cell culture All cell lines used and derived by different approaches in this study are listed in Supplementary Table 1. Detailed information about the experimental design, materials and reagents is presented in the Reporting Summary. Primary human adult dermal fibroblasts (HDFa) from three different female donors were obtained from Gibco…

Mouse models C57BL/6J (strain 000664, The Jackson Laboratory) and B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*/-EGFP)Fezh/J (strain no. 026179, The Jackson Laboratory) were used for all experimental procedures. The Npm1c/Flt3-ITD/Cas9 model has been extensively described previously31,57,58. The maximal tumor size allowed by the Home Office license for this project and authorized by the Animal Welfare Ethical…

Plant materials The plant material used in this study was selected from a collection of 733 accessions of wild and domesticated einkorn held at the Wheat Genetics Resource Center (WGRC) at Kansas State University42. To generate reference assemblies, we selected one domesticated einkorn accession (T. monococcum L. subsp. monococcum; TA10622)…

bedGraphToBigWig Install error 1 Hi I am trying to convert BAM file to BedGraph and ultimately to BigWig file. To install bedGraphToBigWig on cluster system, I did: URL=http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64 curl $URL/bedGraphToBigWig > ~/bin/bedGraphToBigWig chmod +x ~/bin/bedGraphToBigWig curl $URL/faToTwoBit > ~/bin/faToTwoBit chmod +x ~/bin/faToTwoBit And to see if bedGraphToBigWig command worked, I…

How to overlay tracks in IGV? 0 I am trying to overlay these four tracks on IGV so that they are color-coded by importance, however the overlay tracks feature isn’t working. When I select Tracks > Overlay Data tracks, a dialogue box pops up saying “overlay tracks by” and the…

Genome Browser for Visualizing Coverage Data, Custom Annotations, and Genome Sequence? 0 I am looking for a genome browser that can do the following: Visualize coverage data, ideally by importing a bigwig file or similar Add a set of custom annotations to the genome by importing a bed file or…

About the value in bigwig file 0 Hi all, I want to compare the peaks to see which condition has more chromatin open and I got advice that I should adjust all the range to the highest value. When I set the min to 2.3, I got this. Is that…

BAM File: Trim Reads So Only First Base Remains 0 I mapped single-end 50-bp reads to a genome and now have BAM files. I need to trim the reads within the BAM file so that only the first base remains (the first base called by the sequencer). Ideally it would…

How to get genes associated with open chromatin regions? 1 Hi all, I ran ATAC-seq pipeline such as nf-core and got output files such as bam, bigwig, broadpeak. Would you suggest a way to get genes associated with open chromatin regions? I used ChIPpeakAnno but for DiffBind. Thank you so…

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…