deepTools
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deeptools
Tools to process and analyze deep sequencing data.
Hi, My issue is somewhat related to #662 Have tried multiple versions, most recent being 3.4.3 with Python 3.8.5 bamCoverage works the majority of the time for my pipeline. But...
Hello, I want to use only a specific region on different chromosomes in my bamfile for bamCoverage or bamCompare. When I specify the regions, sometimes it sticks to the specified...
Hello, How can I plot the heatmap with the fold changes of ChIP-seq occupancy levels of 2 samples?  Thanks
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Dear I'm trying to generate a matrix in order to make metaprofile . the input data are methylation in bigwig format. The problem is that in my matrix a lot...
Hi, I performed the alignmentSieve --ATACshift, before that the bam file was: R1 1107 chr1 3050133 40 **35M** 3050133 **-35** R2 1187 chr1 3050133 40 **35M** 3050133 **35** after the...
Hello, Dear Deeptools Developer, This is Sally, a Master’s student studying Molecular Biotechnology and Bioinformatics. Currently I am doing my internship in bioinformatics. I am writing because I am facing...
Dear deeptools developer, Thanks for developing such a great tool! I recently ran a Cut & Tag experiment(2 X 150bp) and want to use the plots from deeptools to show...
Hello, I used bamCoverage with RPKM normalization to get bigwig files. I then used `pyBigWig.values()` function to view bigwig files in a given genomic region. I noticed all the non-zero...
If I have multiple bam files (replicates), how ```bamCoverage``` work? There used to be a function ```multiBamCoverage``` but it has been removed from the latest deeptools (3.5.5). How do you...
