deepTools
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deeptools
Tools to process and analyze deep sequencing data.
Hello, I’m encountering errors when processing the output of alignmentSieve with samtools sort and bgzip in a specific workflow. The error occurs only when using a filtered BAM (clean.bam) as...
Hi. I try to compare two .bam files. The inputs are sorted and indexed. They were aligned to the same reference genome: GRCh38. I assume that It is important to...
Hi there, thank you for your work on deeptools! I have multiple colleagues who use the `computeMatrix` (reference-point) and `plotHeatmap` tools extensively in their work. Yet, I'm noticing that `computeMatrix`...
Hi, I am trying to plot the individual base modifications in a modkit processed mod-bam file. My data very much looks like this; chr1 596159 596159 0.024414063 chr1 596189 596189...
Why is the DNA methylation level in the output DNA methylation plot from computeMatrix so low, even though I converted my bedGraph file to a bigWig file and used this...
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR contain new feature? - [ ] Does the PR contain...
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR contain new feature? - [ ] Does the PR contain...
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR contain new feature? - [ ] Does the PR contain...
@WardDeb `.npz` is in `.gitignore`. Neverthless, I added a required `.npz` test input file.
**Welcome to deepTools GitHub repository! Please check the following regarding your pull request :** - [ ] Does the PR contain new feature? - [ ] Does the PR contain...