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How can bamcompare handle spike-in normalized chip-seq data？

1

I see that there is a scalefactor for bamcompare to normalize reads between experiment group and control group, but where can I put my correction-factor generated by spike-in tags?

yeast0326

Correct relabel samples parameter

3

computeMatrixOperations relabel should have `--sampleLabels` instead `--sample` in usage description. **Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR...

janoppelt

Sample data for testing

1

**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...

maojn

bamCoverage does not accept trancriptome mapped alignment files

2

Hi, I am using transcriptome mapped alignment files and I wanted to visualize them on IGV in bigwig format. However, as far as I understand, bamCoverage is not able to...

kaltinel

Left over 0 in plotProfile

1

There's a random 0 left over when plotProfile adds a title: plotProfile -m mat.gz -out profile.png --plotType se --labelRotation 45 --plotHeight 15 --plotWidth 15 -T "Average Profile" This is probably...

dpryan79

Extend nucleotides to be counted on bamCoverage "--MNase" argument.

1

Hi, bamCoverage "--MNase" is a good argument, but it only counts 3 nucleotides at the center of each fragment. Is it possible to add another argument to specify an offset...

chesterlee7246

plotting error with computeGCBias function

4

Hi, I have a problem with the computeGCBias function. I installed deeptools with `conda create -n deeptools_env -c bioconda deeptools` and I successfully ran computeGCBias for a number of datasets....

AlcaArctica

The deeptools sample data file no longer available in galaxy website

6

`If you would like to try out the protocols with sample data, go to deepTools Galaxy –> “Shared Data” –> “Data Libraries” –> “deepTools Test Files”. Simply select BED/BAM/bigWig files...

tongtong1993

deeptools cluster by logfc in peak regions

2

**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...

das2000sidd

Intribuing behavior of plotCorrelation with mixture of single-end and paired-end datasets

4

Hello I am using deepTools 3.3.2 with Python 3.7.0 I noticed something intriguing when using plotCorrelation (after multiBigwigSummary), specifically when the various bigwigs are a mixture of single and paired-end...

AlexBlais74