deepTools
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deeptools
Tools to process and analyze deep sequencing data.
Hello, I have DNA methylation bigwigs with single cytosine resolution and I am trying to reduce the size of the files by averaging the methylation values across bins. I found...
**This PR:** Adds the argument `--keepTags` in [alignmentSieve.py](https://github.com/deeptools/deepTools/blob/master/deeptools/alignmentSieve.py) to keep the original alignment tags in the filtered/shifted/output BAM. This can be useful to distinguish between read pairs from different secondary...
Hi, I'm having problems with plotHeatmap and K-means clustering. I am not able to reproducibly plot heatmaps, as the numbers of lines in them varies between runs, even when giving...
[--filterRNAstrand](https://github.com/deeptools/deepTools/blob/83f192947606c62028717f0e0824dc23a07536dc/deeptools/alignmentSieve.py#L90) documentation is misleading. The actual filtration, from what I've tested, actually works as documented for bamCoverage `--filterRNAstrand` (see [bamCoverage --filterRNAstrand](https://github.com/deeptools/deepTools/blob/83f192947606c62028717f0e0824dc23a07536dc/deeptools/bamCoverage.py#L104). It indicates this: `Selects RNA-seq reads (single-end or paired-end)...
Hi, I generated bigwig file for methylation data to plot average methylation level on set of genomic regions but I am getting the below mentioned error. I am using deeptool...
python version 3.8 deepTools version 3.5.1 I wanted to compute the coverage of a paired bam file, and got an error about fragment start being greater than fragment end. After...
How can I use bamCoverage to calculate RPM? deeptools version is 3.5.1. Thanks!
Hello, While using `plotHeatmap` to create heatmap for a TF ChIP-seq dataset, I got inconsistent peak around TSS between 'TSS +-3kb region' and 'gene body(TSS-TES) region'.  In figure A,...
I need to plot PCA between my samples(BAM format) using multiBamSummary and plotPCA, however I don't see any options to normalize my samples neither in multiBamSumamry nor in plotPCA.
