Tag: deepTools

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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