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author iuc
date Sat, 15 Feb 2014 15:43:39 -0500
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16:d9a0a017896a 17:35a80f8dda5c
1 ======================== 1 ========================
2 Galaxy deeptools wrapper 2 Galaxy wrapper for MACS2
3 ======================== 3 ========================
4 4
5 deepTools are user-friendly tools for the normalization and visualization of 5 With the improvement of sequencing techniques, chromatin immunoprecipitation
6 deep-sequencing data. 6 followed by high throughput sequencing (ChIP-Seq) is getting popular to study
7 They address the challenge of visualizing the large amounts of data that are now 7 genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq
8 routinely generated from sequencing centers in a meaningful way. 8 analysis method, we present a novel algorithm, named Model-based Analysis of
9 To do so, deepTools contain useful routines to process the mapped reads data 9 ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures
10 through removal of duplicates and different filtering options to create coverage 10 the influence of genome complexity to evaluate the significance of enriched ChIP
11 files in standard bedGraph and bigWig file formats. deepTools allow the creation 11 regions, and MACS improves the spatial resolution of binding sites through
12 of normalized coverage files or the comparison between two files 12 combining the information of both sequencing tag position and orientation.
13 (for example, treatment and control). Finally, using such normalized and 13 MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
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 14
27 15
28 ======== 16 ============
29 Citation 17 Installation
30 ======== 18 ============
31 19
32 deeptools are currently under review. In the meantime please refere to https://github.com/fidelram/deepTools. 20 It is recommended to install this wrapper via the `Galaxy Tool Shed`.
21
22 .. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
33 23
34 24
35 ======= 25 =======
36 History 26 History
37 ======= 27 =======
38 28 - v2.0.10.1: Initial public release
39 - v1.0: Initial public release 29 - v2.0.10.3: add "broad peaks" options
40 30
41 31
42 Licence (MIT) 32 ====================
43 ============= 33 Detailed description
34 ====================
44 35
45 Permission is hereby granted, free of charge, to any person obtaining a copy 36 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst
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 37
52 The above copyright notice and this permission notice shall be included in
53 all copies or substantial portions of the Software.
54 38
55 THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 39 ===============================
56 IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 40 Wrapper Licence (MIT/BSD style)
57 FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 41 ===============================
58 AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 42
59 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 43 Permission to use, copy, modify, and distribute this software and its
60 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN 44 documentation with or without modifications and for any purpose and
61 THE SOFTWARE. 45 without fee is hereby granted, provided that any copyright notices
46 appear in all copies and that both those copyright notices and this
47 permission notice appear in supporting documentation, and that the
48 names of the contributors or copyright holders not be used in
49 advertising or publicity pertaining to distribution of the software
50 without specific prior permission.
51
52 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
53 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
54 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
55 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
56 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
57 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
58 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
59 OR PERFORMANCE OF THIS SOFTWARE.
60