deepTools
deepTools copied to clipboard
deeptools
Tools to process and analyze deep sequencing data.
Hi Deeptools developers, I noticed that bamCoverage --ignoreDuplicates calculates the scaling factor using the total number of mapped reads instead of the number after duplicate removal, which is odd. Additionally,...
- [x] Search whether this issue (or a similar issue) has been solved before using the search tab above. Link the previous issue if appropriate below. - [x] Paste your...
Hi, thanks for this very useful tool! For my current use case, I would find it useful to also specify x-axis limits different from upstream/downstream specified in `computeMatrix`. This would...
### Relevant File: [/galaxy/wrapper/plotEnrichment.xml](https://github.com/deeptools/deepTools/blob/master/galaxy/wrapper/plotEnrichment.xml) ### Issue: The Galaxy deeptools plotEnrichment tool takes two files, a BAM file and a BED file, and finds reads in the BAM file in the...
I don't know if this is really possible, but if people have a LOT of regions or a large BED file then populating `TASKS` is quite slow. Maybe there's a...
Hi Deeptools team, After all these years using Deeptools, I am still confused with some BamCoverage options for reads processing (extend, center, mnase, offset...), specially when it comes to combine...
This is not an issue, but a suggestion of an additional normalisation option. I've been processing from iCLIP data recently, and the normalisation there seems to be a signal-background-ratio, where...
hi, everyone! I recently analyzed the chip-seq data for histone marks. I am very confused with the results for `pheatmap` and `multibigwigsummary` results. I plotted the enrichment level in the...
Hello, I was wondering if plotFingerprint supports bigwig input files? The documentation mentions using bigwigs or indexed BAM files as input: https://deeptools.readthedocs.io/en/develop/content/tools/plotFingerprint.html (_plotFingerprint randomly samples genome regions (bins) of a...
deepTools version: deeptools/3.5.0 python version: Python 2.7.12 Command: `alignmentSieve --numberOfProcessors max --ATACshift --blackListFileName ${blacklist}/hg38-blacklist.v2.bed --bam ${sample}.blacklist-filtered.bam -o ${sample}-shifted.bam` head of output bam file: ``` SRR11960172.31746147 163 chr1 3000138 33 48M...
