Dear All,<div><br></div><div>We have been trying to upload Quantitative Data for more than one experiment to GBrowse locally installed on Mac OS X. In order to do this we've been following the Administrative tutorial according to which gff3 file contains the data to be displayed. </div>
<div><br></div><div>Ex :</div><div><br></div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>LOC_Os01g01010<span class="Apple-tab-span" style="white-space:pre"> </span>microarray_exp<span class="Apple-tab-span" style="white-space:pre"> </span>1903<span class="Apple-tab-span" style="white-space:pre"> </span>9817<span class="Apple-tab-span" style="white-space:pre"> </span>5.758830<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Name=Seedling</div>
<div><br></div><div>Likewise we've appended the above file with the data of another experiment, the sample data for which is like :</div><div><br></div><div>Chr1<span class="Apple-tab-span" style="white-space:pre"> </span>LOC_Os01g01010<span class="Apple-tab-span" style="white-space:pre"> </span>microarray_exp<span class="Apple-tab-span" style="white-space:pre"> </span>1903<span class="Apple-tab-span" style="white-space:pre"> </span>9817<span class="Apple-tab-span" style="white-space:pre"> </span>14.578833<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>.<span class="Apple-tab-span" style="white-space:pre"> </span>Name=Root</div>
<div><br></div><div>The modifications done in the conf file are as follows : </div><div><br></div><div>[TransChip1]</div><div>feature = microarray_exp</div><div>glyph = graded_segments</div><div>graph_type = boxes</div>
<div>fgcolor = red</div><div>bgcolor = orange</div><div>height = 10</div><div>min_score = 0</div><div>max_score = 15</div><div>category = Transcriptional Profile</div><div>key = Seedling</div>
<div><br></div><div>[TransChip2]</div><div>feature = microarray_exp</div><div>glyph = graded_segments</div><div>graph_type = boxes</div><div>fgcolor = red</div><div>bgcolor = orange</div>
<div>height = 10</div><div>min_score = 0</div><div>max_score = 15</div><div>category = Transcriptional Profile</div><div>key = Root</div><div> </div><div>With these data and conf files the display we get in GBrowse is both for Seedling and Root but,the color gradation displayed is the same for both even though the scores provided in the gff3 files differ a lot.Probably, the data is being displayed from the first data set and not from the other. I am also attaching the screen shot of GBrowse interface for the display we are getting.</div>
<div><br></div><div>Kindly suggest what modifications we need to do in Conf and GFF3 files so that different data sets can be displayed with corresponding color gradations.</div><div><br></div><div>Thanking You</div><div>
<br></div><div>Regards</div><div><br></div><div>Tripti</div><div>Junior Research Fellow</div><div>Department of Plant Molecular Biology</div><div>University of Delhi</div><div>India</div>