Tag: deepTools

a strange pattern of repetitive summits

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…

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Index of /~ckern/FAANG_Project/Pig/DeepTools

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  …

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deeptools plotHeatMap – Convert bed files to gene list?

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…

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A genome-scale screen for synthetic drivers of T cell proliferation

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…

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Butterfly eyespots evolved via cooption of an ancestral gene-regulatory network that also patterns antennae, legs, and wings

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,…

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python – Packages Not Found Error: Not available from current channel- Bioconda

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…

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Difference of results with the same input [RNAseq analysis]

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…

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Profiling and functional characterization of maternal mRNA translation during mouse maternal-to-zygotic transition

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…

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How to fix deeptoolsintervals fatal error: python.h? ( Python, Python 3.X )

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…

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The role of ATXR6 expression in modulating genome stability and transposable element repression in Arabidopsis

Significance The plant-specific H3K27me1 methyltransferases ATXR5 and ATXR6 play integral roles connecting epigenetic silencing with genomic stability. However, how H3K27me1 relates to these processes is poorly understood. In this study, we performed a comprehensive transcriptome analysis of tissue- and ploidy-specific expression in a hypomorphic atxr5/6 mutant and revealed that the…

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ChIP-Seq density plot between two groups of genes

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

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Chipseq density plot between two grops of genes

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

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Arrange the size of subplots in plotHeatmap deeptools figure

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…

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computeMatrix in deeptool is Running with no result

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…

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Deeptools: computeMatrix can’t read file

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]…

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A matrix sample for Profile plots and heatmaps of Computematrix, deepTools

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…

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multiBamSummary for unpaired end read?

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…

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Bedfile format deeptools

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…

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computematrix how to set certain TSS

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…

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