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author bgruening
date Tue, 04 Feb 2014 13:45:17 -0500
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1 ======================== 1 This package contains a collection of Galaxy workflows utilising deepTools.
2 Galaxy deeptools wrapper
3 ========================
4 2
5 deepTools are user-friendly tools for the normalization and visualization of 3 See http://www.galaxyproject.org for information about the Galaxy Project.
6 deep-sequencing data.
7 They address the challenge of visualizing the large amounts of data that are now
8 routinely generated from sequencing centers in a meaningful way.
9 To do so, deepTools contain useful routines to process the mapped reads data
10 through removal of duplicates and different filtering options to create coverage
11 files in standard bedGraph and bigWig file formats. deepTools allow the creation
12 of normalized coverage files or the comparison between two files
13 (for example, treatment and control). Finally, using such normalized and
14 standardized files, multiple visualizations can be created to identify
15 enrichments with functional annotations of the genome.
16 For a gallery of images that can be produced and a description
17 of the tools see our poster_.
18
19 .. _poster: http://f1000.com/posters/browse/summary/1094053
20
21 deeptools is developed under here:
22
23 https://github.com/fidelram/deepTools
24
25 For support, questions, or feature requests contact: deeptools@googlegroups.com
26 4
27 5
28 ======== 6 Sample Data
7 ===========
8
9 Sample data can be obtained from http://deeptools.ie-freiburg.mpg.de/library or you
10 can use aligned reads in BAM or SAM format.
11
12
13
29 Citation 14 Citation
30 ======== 15 ========
31 16
32 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. 17 If you use this workflow directly, or a derivative of it, or the associated
18 deepTools wrappers for Galaxy, in work leading to a scientific publication,
19 please cite:
20
21 {publication under review}
33 22
34 23
35 ======= 24 Availability
36 History 25 ============
37 =======
38 26
39 - v1.0: Initial public release 27 This workflow is available on the main Galaxy Tool Shed:
28
29 http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools_workflows
30
31 Development is being done on github:
32
33 https://github.com/fidelram/deepTools
40 34
41 35
42 Licence (MIT) 36 Dependencies
43 ============= 37 ============
44 38
45 Permission is hereby granted, free of charge, to any person obtaining a copy 39 These dependencies should be resolved automatically via the Galaxy Tool Shed:
46 of this software and associated documentation files (the "Software"), to deal
47 in the Software without restriction, including without limitation the rights
48 to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
49 copies of the Software, and to permit persons to whom the Software is
50 furnished to do so, subject to the following conditions:
51 40
52 The above copyright notice and this permission notice shall be included in 41 * http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools
53 all copies or substantial portions of the Software.
54
55 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
56 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
57 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
58 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
59 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
60 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
61 THE SOFTWARE.