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2 Galaxy wrapper for MACS2
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3 ========================
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4
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5 With the improvement of sequencing techniques, chromatin immunoprecipitation
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6 followed by high throughput sequencing (ChIP-Seq) is getting popular to study
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7 genome-wide protein-DNA interactions. To address the lack of powerful ChIP-Seq
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8 analysis method, we present a novel algorithm, named Model-based Analysis of
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9 ChIP-Seq (MACS), for identifying transcript factor binding sites. MACS captures
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10 the influence of genome complexity to evaluate the significance of enriched ChIP
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11 regions, and MACS improves the spatial resolution of binding sites through
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12 combining the information of both sequencing tag position and orientation.
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13 MACS can be easily used for ChIP-Seq data alone, or with control sample with the increase of specificity.
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14
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15
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16 ============
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17 Installation
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18 ============
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19
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20 It is recommended to install this wrapper via the `Galaxy Tool Shed`.
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21
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22 .. _`Galaxy Tool Shed`: http://toolshed.g2.bx.psu.edu/view/modencode-dcc/macs2
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23
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24
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25 =======
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26 History
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27 =======
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28 - v2.0.10.1: Initial public release
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29 - v2.0.10.3: add "broad peaks" options
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30
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31
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32 ====================
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33 Detailed description
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34 ====================
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35
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36 View the original MACS2 documentation: https://github.com/taoliu/MACS/blob/master/README.rst
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37
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38
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39 ===============================
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40 Wrapper Licence (MIT/BSD style)
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41 ===============================
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42
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43 Permission to use, copy, modify, and distribute this software and its
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44 documentation with or without modifications and for any purpose and
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45 without fee is hereby granted, provided that any copyright notices
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46 appear in all copies and that both those copyright notices and this
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47 permission notice appear in supporting documentation, and that the
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48 names of the contributors or copyright holders not be used in
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49 advertising or publicity pertaining to distribution of the software
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50 without specific prior permission.
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51
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52 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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53 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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54 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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55 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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56 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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57 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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58 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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59 OR PERFORMANCE OF THIS SOFTWARE.
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60
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