http://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&feed=atom&action=historyACT IntegratedExample - Revision history2024-03-29T08:33:09ZRevision history for this page on the wikiMediaWiki 1.15.4http://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=609&oldid=prevJustin.jee at 18:20, 23 October 20102010-10-23T18:20:27Z<p></p>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The pink bars correspond to the range of covered values as determined by saturating the files in every possible order.</ins></div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=599&oldid=prevJustin.jee at 15:36, 22 October 20102010-10-22T15:36:28Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Using ACT.py, we get a four-column file which can be plotted in Excel or using R:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Using ACT.py, we get a four-column file which can be plotted in Excel or using R:</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"><pre>python ACT.py --nbins=50 --mbins=0 --radius=5000 gencode.coords PolII.sgr > PolII.out &</pre></ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Agg_wg.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Agg_wg.png]]</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The resulting correlation matrix can be plotted in R using the heatmap function:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The resulting correlation matrix can be plotted in R using the heatmap function:</div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">#! /bin/sh</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">java -Xmx1024m -cp $cp org.gersteinlab.act.BinFileCreator config.txt Mean $bin output/PolII$bin.wig ../PolII.bedGraph4</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=516&oldid=prevJustin.jee at 16:51, 10 September 20102010-09-10T16:51:41Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Aggregation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Aggregation</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>After downloading the agg-py package, it is necessary to download an annotations file with coordinates you want to aggregate over. For this example, we used all transcription start sites as taken from build 18 of the human genome annotated by the gencode project.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>After downloading the agg-py package, it is necessary to download an annotations file with coordinates you want to aggregate over. For this example, we used all transcription start sites as taken from build 18 of the human genome annotated by the gencode project. <ins class="diffchange diffchange-inline">For convenience/testing purposes, we have provided a parsed version of the gencode gene annotations which is compatible with act here:</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">http://act.gersteinlab.org/gencode.coords</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Using ACT.py, we get a four-column file which can be plotted in Excel or using R:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Using ACT.py, we get a four-column file which can be plotted in Excel or using R:</div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=515&oldid=prevJustin.jee at 16:47, 10 September 20102010-09-10T16:47:04Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=514&oldid=prevJustin.jee at 16:46, 10 September 20102010-09-10T16:46:20Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=513&oldid=prevJustin.jee at 16:45, 10 September 20102010-09-10T16:45:47Z<p></p>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=512&oldid=prevJustin.jee at 16:44, 10 September 20102010-09-10T16:44:25Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Saturation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Saturation</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>It is necessary to convert the wig files to bed files without a "signal" component. The following script takes wig files and converts them into bed files, with coordinates representing the regions of the signal track which are above a certain threshold (in this case <del class="diffchange diffchange-inline">0</del>).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>It is necessary to convert the wig files to bed files without a "signal" component. The following script takes wig files and converts them into bed files, with coordinates representing the regions of the signal track which are above a certain threshold (in this case <ins class="diffchange diffchange-inline">20</ins>).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>http://act.gersteinlab.org/wig2bed.pl</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>http://act.gersteinlab.org/wig2bed.pl</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Go to saturation.sh and change the input files to PolII.bed and Stat1.bed. It will also probably be necessary to change the alloted memory (in the second of the final java command in saturation.sh, change the numbers in the second field from 128 to 4096). </ins>Since there are only two signal tracks, the Saturation and Correlation analyses provide overlapping information.</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">[[Image:Saturation_wg_t20.png]]</ins></div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=497&oldid=prevJustin.jee at 01:26, 10 September 20102010-09-10T01:26:25Z<p></p>
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<td colspan='2' style="background-color: white; color:black;">Revision as of 01:26, 10 September 2010</td>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Aggregation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Aggregation</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">After downloading the agg-py package, it is necessary to download an annotations file with coordinates you want to aggregate over. For this example, we used all transcription start sites as taken from build 18 of the human genome annotated by the gencode project.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">Using ACT.py, we get a four-column file which can be plotted in Excel or using R:</ins></div></td></tr>
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<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:Agg_wg.png]]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Correlation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Correlation</div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=493&oldid=prevJustin.jee at 19:35, 9 September 20102010-09-09T19:35:13Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Correlation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Correlation</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">It </del>is necessary to convert the signal tracks from sgr to wig format. A script which does this can be found here:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">For this example, since we are dealing with signal tracks rather than SNP positions or a bed file of genomic locations, we will use the correlation tool found in corr-sat-bundle to do the correlation calculation. First, it </ins>is necessary to convert the signal tracks from sgr to wig format. A script which does this can be found here:</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>http://act.gersteinlab.org/sgr2wig.pl</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>http://act.gersteinlab.org/sgr2wig.pl</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The resulting correlation matrix can be plotted in R:</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Once we have converted both the PolII and Stat1 sgr files to wig files, we can change the parameters in correlation.sh so that the input files are "PolII.wig" and "Stat1.wig"</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">In addition, it is important to change config.txt so that the list of genomic regions includes all chromosomes, including mitochondrial sequences. (When the package is first downloaded, all lines except for the one denoting chromosome 22 are commented out).</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">Once both the correlation.sh and config.txt files have been modified, we can run correlation.sh. This will produce an output file with a correlation matrix describing the correlation coefficients between PolII and Stat1 signal.</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The resulting correlation matrix can be plotted in R <ins class="diffchange diffchange-inline">using the heatmap function</ins>:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Corr_wg_heatmap.png]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[Image:Corr_wg_heatmap.png]]</div></td></tr>
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</table>Justin.jeehttp://info.gersteinlab.org/index.php?title=ACT_IntegratedExample&diff=492&oldid=prevJustin.jee at 19:06, 9 September 20102010-09-09T19:06:51Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>http://act.gersteinlab.org/sgr2wig.pl</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>http://act.gersteinlab.org/sgr2wig.pl</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">The resulting correlation matrix can be plotted in R:</ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;">[[Image:Corr_wg_heatmap.png]]</ins></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Saturation</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*Saturation</div></td></tr>
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</table>Justin.jee