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Dear deepTools group, Thanks for your wonderful tool. I used deeptools 3.5.1 and Python 3.9.12. When I was running computeMatrix for ATAC-seq peaks using code: computeMatrix reference-point \ -S ESC_ATAC.bw...

Suger0917

Problem with the HeatMap - it is empty

3

Dear all, I am plotting WGBS data over predefined regions. This is command I used: ``` computeMatrix reference-point -R regions.bed \ -S DNA_3.bw \ DNA_4.bw \ DNA_1.bw \ DNA_2.bw \...

mvukk

Hi . I wish to sort regions by their length without drawing a dashed line. Is it possible to do with plotHeatmap?

Adnanhashim

bamCaverage output .bw file can't be viewed correct by IGV

1

Hi I use the sorted .bam file as input and .bw file is the output, there was no error reported, when using bamCaverage. The sorted .bam file can be viewed...

ShaokunPan

Not able to change xRange and yRange from plotCorrelation

5

Hy!! I have been trying to use plotCorrelation function but I am not able to adjust de x and y axis. This is the code I am using: > multiBamSummary...

iramai

**Welcome to deepTools GitHub repository! Before opening the issue please check that the following requirements are met :** - [ ] Search whether this issue (or a similar issue) has...

aaperez9201

Isolating Clusters From Heatmap Created With DeepTools

2

I successfully created a heatmap using deeptools that contains k means clustering. How would I now isolate the data from those individual clusters?

kherzberger

CountReadsPerBin using bedFile does not return counts in the expected order

3

Hi team, When running `CountReadsPerBin` using a BED file to define the regions, the resulting numpy array **doesn't seem to be sorted** according to the entries in the BED file....

alexbarrera

Add "auto" option to --yMin and --yMax of plotHeatmap

1

In options `--yMin` and `--yMax` of `plotHeatmap` would you consider adding an "auto" option that scales each plot inidividually to its minimum and maximum, respectively? For example, in the plots...

dariober

bamCoverage bin size is variable within a file and between files

4

I'm calling bamcoverage on several bam files and specifying the binsize to 50,000. I expect every file to have identical coordinates (first three columns in bed file), otherwise I wont...

mheskett