Tag: deepTools

Compute matrix skipping many regions stating not found in compute matrix output 0 Hello all I am working on Chip seq data and for generating the TSS Plots when I am computing the matrix it is giving a very long list stating “skipping NR_049895_r4, due to being absent in the…

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…

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…

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)….

Introduction The CRISPR-Cas system is a widely used genome engineering technology because of its simple programmability, versatile scalability, and targeting efficiency (Wang & Doudna, 2023). Although researchers are rapidly developing CRISPR-Cas9 tools, the biggest challenge remains to overcome undesired on- and off-targeting outcomes. Previous studies have reported unintended genomic alterations,…

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…

Wrong in Deeptools : the enrichment of TSS and TES region are similar when using scale-region 0 While using plotProfile to create enrichment for a Pol cut-tag dataset, I got similar enrichment peak around TSS and TES which actully will show higher enrichment in TSS than TES. So could someone…

Name Last modified Size Description Parent Directory   –   python-deeptools_3.3.2+ds-2.debian.tar.xz 2020-02-08 20:23 5.2K   python-deeptools_3.3.2+ds-2.dsc 2020-02-08 20:23 2.3K   python-deeptools_3.3.2+ds.orig.tar.xz 2020-01-24 14:18 23M   python-deeptools_3.5.0-1.debian.tar.xz 2020-10-28 16:25 5.6K   python-deeptools_3.5.0-1.dsc 2020-10-28 16:25 2.3K   python-deeptools_3.5.0.orig.tar.xz 2020-10-28 16:25 23M   python-deeptools_3.5.1-1.debian.tar.xz 2021-10-18 18:17 5.7K   python-deeptools_3.5.1-1.dsc 2021-10-18 18:17 2.3K  …

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…

Parasite culture, maintenance, synchronization and transfection The DiCre-expressing P. falciparum clone II3 (ref. 10) was maintained in human A+ erythrocytes at 37 °C in Roswell Park Memorial Institute 1640 medium containing AlbumaxII (Invitrogen) supplemented with 2 mM l-glutamine. Parasites were either synchronized by sorbitol treatment or by purifying mature schizont stages using…

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…

I am following this Galaxy tutorial to analyze Tn-Seq data: (Essential genes detection with Transposon insertion sequencing). This transposon inserts at TA sites. After mapping with Bowtie2, I ran bamCoverage (1 nt window and only report the 5’ end of the reads (position 1)). Inspection of the output bedgraph doesn’t…

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…

Okay, first things first Please I am in hurry and need help Slow down and think again what you are doing. I used MACS Used MACS for what? (BTW, convert SAM to BAM and save some space. Just a suggestion). I’m sure you wanted to find out ChIP enriched regions,…

Abstract Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as…

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…

Visualisation of accessible regions in single cell atacseq data 0 Hi, I want to have an overall visualisation for accessible regions of my interest similar as what plotHeatmap (deeptools) can provide. However, this has become tricky as for this data I just have access to peaks matrix and fragments files…

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”,…

Heatmap ChIP-seq average signal 1 Hey everybody! I am aiming to generate a heatmap for the average signal of a certain histone mark across all gene coding regions, with TSS as the reference point. I am already aware of how to produce such plots using plotProfile and plotHeatmap from the…

This is largely how our group uses them to account for genome-wide shifts, as done in this study. If we don’t normalize the tracks this way, they look largely identical, as the binding profiles are largely similar, just very diminished genome-wide. We also normalize the scaling factors to each other…

To normalize ChIP-seq data with a separate-species spike-in, I’m following the advice described in this GitHub issue: Align to spiked-in species. Compute scaling factor (e.g., multiBamSummary … –scalingFactors). Note, you should have a look at some of the samples to ensure that the spiked-in species has vaguely uniform coverage. If…

Chip-Seq and DeepTools 0 Hello, I have Chip-Seq data for two transcription factor (TF1,TF2) and they have significant numbers of peaks overlapped (MACS2 Peak calling) and I want to plot linear correlation between the signal of TF1 and TF2 peaks in the shared binding sites. Please guide me. Thank you…

Quality control ATAC-seq, using plotFingerprint deepTools 0 Hi all, I am not sure if wf sample has technical issue. Would you please have a comment? Thank you so much! plotFingerprint -b *.bam –labels mf wf –minMappingQuality 30 –skipZeros -T “Fingerprints of different samples” –plotFile fingerprints.png –outRawCounts fingerprints.tab deeptools • 81…

bamCoverage fails in bam files with large number of small contigs in headers 0 Hi, I plan to use bamCoverage from Deeptools to get bw files, but it looks like the thread is dead as it never finishes (no errors). I have hundred of thousands of short unlocalized/random contigs in…

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)…

Recommended normalization procedure for CUT&Tag coverage file 1 Hi! I am performing CUT&Tag data analysis, and I am currently generating a coverage file using bamCoveragefrom the deepTools suite. For general best practice, what would be the best normalization method? I am currently using CPM but I am unsure if this…

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…

How to interpret heatmap using plotheatmap from deeptools? 1 The heatmap indicates by color the amount of signal (whatever this is, RPKM, TPM, normalized counts…) in a windows of +/- 3000bp around the TSS which is the center. The more blue the more signal, the more red the less signal….

Establishment of Zfp296-deficient ESCs The expression of Zfp296 during ESC differentiation into trophectoderm was examined using the ZHBTc4 ESC line, in which expression of Pou5f1 encoding Oct3/4 can be downregulated by tetracycline20. As shown in Supplementary Fig. 1a, Zfp296 expression rapidly decreased, suggesting that Zfp296 is downstream of Oct3/4. To generate…

Methods to integrate ATAC-seq and RNA-seq 0 Hi all, I found many papers doing this integration, so I am not sure which one is the best practice. Would you suggest your favorite paper or a tutorial to do this? Especially the tools to perform the integration. There is a paper…

(A) Volcano plot of log2FC of RNA levels (FXS vs TD). Statistically significant changes (P value <0.0002) are shown as blue dots (down-regulated) and red dots (up-regulated). Gray dots refer to unchanged RNAs. (See also Dataset S2). (B) Histograms for TPM values for RNAs that are up or downregulated in…

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…

How to make the profile line of `deepTools::plotHeatmap` more smooth? 1 Why the profile line has so many wiggles?How to make the profile line more smooth?I assume there are some peaks in the .bed file that are highly repeated, how can I delete those peaks?Thanks a lot computeMatrix reference-point –referencePoint…

Junior Bioinformatician position in BiNGS   We are seeking a junior bioinformatician for the Tisch Cancer Institute Bioinformatics for Next Generation Sequencing (BiNGS) core, to lead transcriptomics and epigenetics data analysis projects related but not limited to cancer biology, skin biology, developmental biology, diabetes, and neuron biology.   The mission…

Principal component analysis using plotPCA of deepTools 0 Hello everyone, I want to find PCA plot for multiple bam files. I used deep tool’s multiBamSummary to find signal coverage over genomic bins. Then, I supplied the output compressed numpy array(.npz) file to the plotPCA of deeptools. I got the required…

Hi! Does anyone know how to download low mappability regions from UCSC for computeGCBias? In deepTools documentation, it said, “You can download the mappability tracks for different read lengths from UCSC, e.g. for mouse and human.” When I go to UCSC hgdownload.cse.ucsc.edu/gbdb/mm10/bbi/, there are different files, which one should I…

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”,…

Phylogenetic tree construction Tree diagram showing relationships between CDK proteins was constructed from a multi-sequence alignment (MSA) using Geneious95. The “Geneious Aligner”, was used to generate the MSA, and the neighbor joining method was used to construct the tree. All default parameters were used except where otherwise indicated. Combinatorial CRISPR…

Normalization of ChIP-seq results with deepTools 0 Hello everyone! I`m trying to visualize ChIP-seq data with deepTools. I used the following commands: bamCoverage (normalization) -> bigwigCompare (normalization against input) -> computeMatrix -> plotProfile As a result I got this figure. Green and yellow plots are for treatment samples replicas, blue…

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…

Nakamura, T. et al. Molecular mechanisms underlying the exceptional adaptations of batoid fins. Proc. Natl Acad. Sci. USA 112, 15940–15945 (2015). Article  ADS  CAS  PubMed  PubMed Central  Google Scholar  Turner, N. et al. The evolutionary origins and diversity of the neuromuscular system of paired appendages in batoids. Proc. Biol. Sci….

To perform gc content bias corrections between atac-seq technical replicates 0 HI. I am conducting an atac-seq data analysis. I would like to proceed with the GC content bias correction in atac-seq data between the three replicates. I would like to proceed with ComputeGCBias and CorrectGCBias of deeptools or after…

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,…

How to normalise ChIP-Seq samples using deeptools 0 I was wondering what is the best approach to normalising Chip-seq samples using the deeptools software. In our data set we’re using an antibody to pull down specific regions of the genome. But when I do the coverage plot I already get…

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…

Cell culture Human lung adenocarcinoma cells A549 expressing human ACE2 (A549-ACE2, NR-53821) were acquired from BEI Resources. They were maintained in DMEM/F-12 (1:1, Corning) medium supplemented with 10% FBS (GeneDepot) and blasticidin (100 μM). Normal A549 cells were purchased from ATCC (CCL-185) and cultured in DMEM/F-12 (1:1, Corning) supplemented with 10%…

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…

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…

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…

Can ChiPseeker be as highly customizable as “computeMatrix”? for example if I want to plot the distribution of genes on the TAD boundary? 0 @8f91699d Last seen 21 hours ago Hong Kong It’s like “computeMatrix” in deeptools, computeMatrix scale-regions -R TAD.boundaries.bed -S gene.density.bw gives the distribution of the eigenvalues (in…

bam file to .bedgraph 4 I have bam files and i need to convert them to .bedgraph format for my further analysis please help me in this issue? RNA-Seq ChIP-Seq Galaxy R genome • 9.8k views Your questions is lacking a couple of details such as what’s the goal of…

Walker, M. J. et al. Disease manifestations and pathogenic mechanisms of Group A Streptococcus. Clin. Microbiol. Rev. 27, 264–301 (2014). Article  PubMed  PubMed Central  Google Scholar  Carapetis, J. R., Steer, A. C., Mulholland, E. K. & Weber, M. The global burden of group A streptococcal diseases. Lancet Infect. Dis. 5,…

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…

Gupta, A., Rico-Medina, A. & Cano-Delgado, A. I. The physiology of plant responses to drought. Science 368, 266–269 (2020). Article  CAS  PubMed  Google Scholar  Hu, H. & Xiong, L. Genetic engineering and breeding of drought-resistant crops. Annu Rev. Plant Biol. 65, 715–741 (2014). Article  CAS  PubMed  Google Scholar  Ashraf, M….

deepTools bamCompare – RPGC normalisation not supported? 0 Working with ChIP-Seq data, I am looking into the various normalisation options available on bamCompare (version 3.5.0) to produce a bedgraph of log2(chip/input) values. RPGC is given as an option in the documentation, however I get the following error: RPGC normalization (–normalizeUsing…

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…

Signac/DeepTools data exchange 0 Hi all, I’m trying to analyze some DOGMA single cell data (GEX+ ATAC). I have been following the tutorials from Seurat + Signac packages to analyze the ATAC part of the data (this one and this one), and so far everything is working fine.My problem is…

How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using `deepTools`? 0 Hello, How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples using deepTools? Thanks a lot. deepTools • 20 views • link 2…

Pearson correlation coefficients of histone modifications at specific region 1 Not exactly what you want, but deepTools has a whole bunch of functionality that still gets at that question. Especially the plotHeatmap function Login before adding your answer. Traffic: 2719 users visited in the last hour Read more here: Source…

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…

Problem with the output of Deeptools PlotProfile: a strange pattern of repetitive summits 0 Hi! I am trying to plot DNA binding profiles of my ChIP-seq bw files using Deeptools plotProfile. I generated the matrix using the computeMatrix reference-point. I used some publicly available bed files as my regions of…

Name Last modified Size Description Parent Directory   –   H3K4me3_Liver_P348.bw 2016-06-24 10:33 60M   H3K4me3_Liver_P348_vs_Input.bw 2016-06-24 20:31 120M   H3K4me3_Liver_P350.bw 2016-06-24 10:37 78M   H3K4me3_Liver_P350_vs_Input.bw 2016-06-24 21:09 128M   H3K4me3_MultiBigwigSummary.npz 2016-06-24 13:44 17M   H3K4me3_Spleen_P348.bw 2016-06-24 10:40 67M   H3K4me3_Spleen_P348_vs_Input.bw 2016-06-24 21:50 128M   H3K4me3_Spleen_P350.bw 2016-06-24 10:43 66M  …

I might suggest limiting your search to genes: gtf2bed < Mus_musculus.GRCm38.102.gtf | grep -w “gene” > sorted-mm10.genes.bed But that’s up to you. Otherwise, I think you may also get transcripts/exons, which may be more than you want. Again, up to you. If hnf4a-ko-downreg-clusters.bed is the file containing peaks, as described…

Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar  Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…

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,…

Using a Mac with M1 chip, I’m trying to install the following Bioconda packages: cutadapttrim-galoresamtoolsbedtools.htseq.bowtie2.deeptools.macs2 I’ve been able to install picard and fastqc with no issues, but all others turn out one of two error messages: PackagesNotFoundError: The following packages are not available from current channels: or Found conflicts! Looking…

Difference of results with the same input [RNAseq analysis] 0 Hello! I am trying to optimize the treatment of some RNAseq files by splitting the input reads into several files. I am comparing the results I have obtained with: the reads input as one file the split input as several…

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…

Problem : ( Scroll to solution ) I tried installing pip3 install deeptoolsintervals the error is: deeptoolsintervals/tree/tree.c:1:20: fatal error: Python.h: No such file or directory compilation terminated. error: command ‘/usr/bin/x86_64-linux-gnu-gcc’ failed with exit code 1 I have Ubuntu 16.04.7 and Python versions installed: ls /usr/bin | grep python dh_python2 dh_python3…

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…

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…

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…

Arrange the size of subplots in plotHeatmap deeptools figure 1 Hi all, I am trying to generate a 10×10 (10 bw files + 10 bed files) figure using deeptools but I am having trouble arranging the size of subfigures. I want the subfigures in the same size but if I…

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]…

A matrix sample for Profile plots and heatmaps of Computematrix, deepTools 0 Hi everyone, I have a count matrix from feature counts and of course, couple of peak (.bed) files. I want to visualize the peaks all together to show the coverage and overall comparing. I was going to use…

Hello everyone, I am using multiBamSummary to computes read coverages for many bam files. multiBamSummary bins –bamfiles *.bam -out readCounts.npz –outRawCounts readCounts.tab However, I got errors as below. May I get help please?? [E::bgzf_read] Read block operation failed with error 2 after 0 of 4 bytes Traceback (most recent call…

Bedfile format deeptools 1 Hello everyone, Using deeptools I am trying to plot the enrichment in Genebody and TSS for this we have to give one BED file region of interest in computeMatrix. I am bit confused about the format based on a thread in biostar TSS metaprofile using Deeptoolsbased…

computematrix how to set certain TSS 1 how to set certain TSS deeptools computematrix, I want to visualize the certain gene’s TSS up/downstream instead of whole gene,but how can I do it ? thanks. deeptools • 34 views You probably want the reference-point mode as described here. You will also…