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1 ========================
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2 Galaxy deeptools wrapper
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3 ========================
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4
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5 deepTools are user-friendly tools for the normalization and visualization of
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6 deep-sequencing data.
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7 They address the challenge of visualizing the large amounts of data that are now
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8 routinely generated from sequencing centers in a meaningful way.
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9 To do so, deepTools contain useful routines to process the mapped reads data
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10 through removal of duplicates and different filtering options to create coverage
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11 files in standard bedGraph and bigWig file formats. deepTools allow the creation
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12 of normalized coverage files or the comparison between two files
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13 (for example, treatment and control). Finally, using such normalized and
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14 standardized files, multiple visualizations can be created to identify
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15 enrichments with functional annotations of the genome.
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16 For a gallery of images that can be produced and a description
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17 of the tools see our poster_.
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18
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19 .. _poster: http://f1000.com/posters/browse/summary/1094053
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20
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21 deeptools is developed under here:
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22
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23 https://github.com/fidelram/deepTools
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24
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25 For support, questions, or feature requests contact: deeptools@googlegroups.com
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26
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27
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28 ========
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29 Citation
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30 ========
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31
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32 deeptools are currently under review. In the meantime please refere to
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33
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34
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35 =======
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36 History
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37 =======
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38
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39 - v1.0: Initial public release
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40
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41
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42 ===============================
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43 Wrapper Licence (MIT/BSD style)
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44 ===============================
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45
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46 Permission to use, copy, modify, and distribute this software and its
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47 documentation with or without modifications and for any purpose and
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48 without fee is hereby granted, provided that any copyright notices
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49 appear in all copies and that both those copyright notices and this
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50 permission notice appear in supporting documentation, and that the
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51 names of the contributors or copyright holders not be used in
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52 advertising or publicity pertaining to distribution of the software
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53 without specific prior permission.
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54
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55 THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
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56 WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
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57 WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
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58 CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
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59 OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
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60 OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
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61 OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
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62 OR PERFORMANCE OF THIS SOFTWARE.
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63
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