Questions tagged [deeptools]

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Metagene analysis with deepTools; 5UTR-CDS-3UTR and Exon-Intron-Exon

I have some PCR-CLIP data. PAR-CLIP identifies targets for RNA binding proteins. I am interested to build metagene profile so that transcript wide binding pattern can be compared. What I am mostly ...
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1 vote
1 answer
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Clarification regarding (deepTools) bamCoverage output

Im using bamCoverage on a file and ive set the bin size to 1 but also normalizing using RPKM for defined regions using a bedgraph file. The output from bamCoverage however is in binned segments each ...
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Setting scale of profile plot from zero for chip seq profile plot

Figure from this paper which shows a profile plot in figure4 first figure. .This i guess is made using deeptools perhaps. Meanwhile When i tried to do similar plot the scale doesn't start from 0. So ...
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2 votes
1 answer
28 views

How to calculate the number of peaks that are upstream/downstream of some other peaks

I have 3 histone marks,I have used Macs2 for peak calling and diffBind to analyze the peaks. I was wondering if you know any way to calculate the peak numbers of one specific histone mark that occur ...
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2 votes
2 answers
363 views

How to convert BAM file to bigWig in Python?

I am manipulating some BAM files using pysam package which seems to be very fast and handy. However, I ran into problem when I am trying to generate bigWig files ...
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1 vote
1 answer
108 views

merge the matrix from computematrix of deeptools

I have several matrix from computematrix of deeptools. I need to merge two of them using "computeMatrixOperations cbind -m input1.mat.gz input2.mat.gz -o output.mat.gz" but I am running to error "/...
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1 vote
1 answer
175 views

plot correlation between several bam files

I have several mab files from medip-seq. they supposed to be replicates and I have to draw their correlation. First I used multiBamSummary from deeptools to merge all the bam files based on bi/bed. ...
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1 answer
52 views

Pol_II genome wide occupancy analysis

I would like to know how to perform this global Pol II occupancy which is shown here: Paper Figure 1G So in this figure they are analysing the Pol II occupancy in Control,PAF1 KD and LEO1. I have ...
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0 votes
1 answer
57 views

multiBamSummary output chromosome region annotate issue

I was looking how to take readcount from ATAC seq data , this post which suggested to use bedtools and featurecounts to take out readcounts .But multiBamSummary seems to be pretty straight forward. ...
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  • 1,662
2 votes
1 answer
129 views

RPGC normalisation creates artefacts at centromere

I am studying ChIP-Seq data in HeLa cells and I've started using the RPGC normalisation of deepTool's bamCoverage. MACS2 also uses this normalisation for its peak calling. I am seeing a large number ...
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1 vote
0 answers
23 views

scaling algorithm of deeptools

I am using deeptools to generate a metagene plot. I am wondering how the deeptools scale genes if the size of genes is shorter than bin size. For example, if my bin size is 1000 bp and the gene is ...
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2 votes
1 answer
185 views

Different outputs of computeMatrix depending on binsize

I'd like to output a figure in +/-1kb around a center using computeMatrix as following command: ...
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5 votes
1 answer
173 views

Dealing with absence of coverage

In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
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3 votes
1 answer
109 views

IGV faster loading remote bigWig files

I noticed remote bigWig files (http URL) take sometimes about 1 minute to load on IGV. Once they loaded, jumping from one region to another can also take several seconds. My understanding is that ...
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7 votes
1 answer
727 views

What unit do I get on the y-axis of a metagene profile plot?

I start with a sorted and indexed bam file ("mapped.bam") representing the mapping of small reads on a reference genome, and a bed file ("genes.bed") containing the coordinates of a set of features of ...
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