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plotCoverage - ZeroDivisionError - verbose mode - 3.5.1

1

Deeptools 3.5.1 ``` plotCoverage -b SRR105321441.dedup.bam -p 4 --outRawCounts coverage.tab --plotFile sample_coverage --plotTitle "Sample Coverage" --verbose -o sample_coverage.png ``` ``` File "countReadsPerBin.py", line 713, in get_coverage_of_region multiprocessing.current_process().name, c, c /...

chris-cheshire

Keep the same number of rows in heatmap

4

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

shengyongniu

Issues with bamCoverage---very slow with relative big bam files

7

Hi everyone, I use bamCoverage (bamCoverage version: 2.5.3, python version: 2.7.5) to convert sorted bam files to bigwig files for visualization in UCSC genome browser. It usually takes less than...

Ying-Zhou-428

Choose proper normalization method making bigWig files

2

Hello! I have a question about making bigWig files using bamCoverage. When I make bigWig files, all the samples have different mapped reads. And also, there are many different normalization...

dahun73

Hi, thanks for implementing the new function 'dataRange'. I find it very useful. However, I stumbled across an issue and have one feature request: # The issue nan values in...

mirax87

Discarding negative values from input normalized bigwig tracks

1

Hello, I have chip-seq data for several histone marks for which I have created RPKM normalized bigwig tracks. I am now looking at the correlation between them using multiBigwigSummary and...

re2srm

How to sort heatmap of multi samples?

1

Hello, Thank you for giving nice program. I have a question about sorting heatmap. I'm using '--sortUsing' option when I draw heatmap. In manual, there is no detailed explanation about...

dahun73

Current behavior is to produce a plot with the number of samples equal to the number of labels provided, presumably matched by index such that samples may be labelled incorrectly...

adadiehl

deeptools 3.2.1 plotProfile / multiqc

1

Hi, I think there is a small bug in the plotProfile output (v3.2.1) and MultiQC. ``` computeMatrix reference-point \\ --referencePoint TSS \\ -R $geneBed \\ -S ${bigwig} \\ -o ${prefix}_matrix.mat.gz...

nservant

I met problems in computeMatrix

3

Hi, I met problems when I run the computeMatrix program. The errors are as following: File "miniconda/computeMatrix", line 14, in main(args) File "/miniconda/lib/python3.7/site-packages/deeptools/computeMatrix.py", line 421, in main hm.computeMatrix(scores_file_list, args.regionsFileName, parameters,...

wuheng9