Questions tagged [deeptools]
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Warning message related to tensorflow package when trying to run deepbgc bioinformatics tool
I have come across some related issues pertaining to this tensorflow warning but none related specifically to deepbgc I have created a conda environment and have installed onto it the bioinformatics ...
pip installation within conda env: Error downgrading scikit-learn - WARNING: No metadata
I am trying to get the bioinformatics tool deepbgc up and running. Now I have created a conda environment and have currently ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 "/...
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. ...
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 ...
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. ...
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 ...
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 ...
Different outputs of computeMatrix depending on binsize
I'd like to output a figure in +/-1kb around a center using computeMatrix as following command: ...
Dealing with absence of coverage
In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
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 ...
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 ...