Questions tagged [deeptools]
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18 questions
2
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1
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417
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Error while running computeMatrix command in Deeptools
I am trying to get computeMatrix for bigwig file in specific genomic region using deeptools.
Below is the code I am using
...
- 21
1
vote
1
answer
1k
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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 ...
- 101
2
votes
1
answer
936
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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 ...
- 101
1
vote
0
answers
684
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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 ...
- 31
1
vote
1
answer
175
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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 ...
0
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0
answers
205
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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 ...
- 1,854
2
votes
1
answer
36
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 ...
- 125
2
votes
2
answers
570
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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 ...
- 887
1
vote
1
answer
247
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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 "/...
- 125
1
vote
1
answer
308
views
plot correlation between several bam files
I have several mab files from medip-seq. They are 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....
- 125
0
votes
1
answer
110
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 ...
- 1,854
1
vote
1
answer
93
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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. ...
- 1,854
2
votes
1
answer
253
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 ...
- 412
1
vote
0
answers
32
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 ...
- 11
2
votes
1
answer
237
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Different outputs of computeMatrix depending on binsize
I'd like to output a figure in +/-1kb around a center using computeMatrix as following command:
...
- 21
5
votes
1
answer
191
views
Dealing with absence of coverage
In my snakemake workflow, I use deeptools bamCoverage (in a make_bigwig rule), then ...
- 3,170
3
votes
1
answer
173
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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 ...
- 2,364
7
votes
1
answer
891
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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 ...
- 3,170