| deepTools address the challenge of visualizing the large amounts of data that are now routinely generated from sequencing centers in a meaningful way. To do so, deepTools contain useful routines to process the mapped reads data through removal of duplicates and different filtering options to create coverage files in standard bedGraph and bigWig file formats. deepTools allow the creation of normalized coverage files or the comparison between two files (for example, treatment and control).
Finally, using such normalized and standardized files, multiple visualizations can be created to identify enrichments with functional annotations of the genome. For a gallery of images that can be produced and a description of the tools see http://f1000.com/posters/browse/summary/1094053 https://github.com/fidelram/deepTools Wikipage: https://github.com/fidelram/deepTools/wiki Requirements: python 2.7, (numpy and scipy will be installed automatically via the Galaxy Tool Shed) Repository-Maintainer: Björn Grüning Repository-Development: https://github.com/fidelram/deepTools/ |
| Name | Version | Type | |
|---|---|---|---|
| deepTools | 1.5.11 | package | |
| python | 2.7.10 | package | |
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| to see whether your samples should be normalized for GC bias | 1.5.11.0 | any | |
| normalizes and compares two BAM files to obtain the ratio, log2ratio or difference. (bam2bigwig) | 1.5.11.0 | any | |
| correlates pairs of BAM files | 1.5.11.0 | any | |
| Given a BAM file it samples several regions to estimate the paired-end fragment length | 1.5.11.0 | any | |
| uses the output from computeGCBias to generate corrected BAM files | 1.5.11.0 | any | |
| correlates pairs of BigWig files | 1.5.11.0 | any | |
| preparation step to plot a heatmap or a profile | 1.5.11.0 | any | |
| creates a profile plot for a score associated to genomic regions | 1.5.11.0 | any | |
| normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference | 1.5.11.0 | any | |
| creates a heatmap for a score associated to genomic regions | 1.5.11.0 | any | |
| generates a coverage bigWig file from a given BAM file. Multiple options are available to count reads and normalize coverage. (bam2bigwig) | 1.5.11.0 | any | |
| plots profiles of BAM files; useful for assesing ChIP signal strength | 1.5.11.0 | any | |