http://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&feed=atom&action=historyFusionSeq List of programs - Revision history2024-03-29T08:11:15ZRevision history for this page on the wikiMediaWiki 1.15.4http://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=1429&oldid=prevAsboner: /* gfrConfidenceValues */2011-07-14T19:20:41Z<p><span class="autocomment">gfrConfidenceValues</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 19:20, 14 July 2011</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 301:</td>
<td colspan="2" class="diff-lineno">Line 301:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Mapped_reads 236549456</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> Mapped_reads 236549456</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This represent the number of PE reads that were mapped. It is possible to determine this number by counting the number of lines in the [[#Mapped Read Format (MRF)|MRF]] file. For example:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This represent the number of PE reads that were mapped. It is possible to determine this number by counting the number of lines in the [[#Mapped Read Format (MRF)|MRF]] file. For example:</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> grep -v AlignmentBlocks file.mrf | wc -l</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> grep -v AlignmentBlocks file.mrf <ins class="diffchange diffchange-inline">| grep -v "#" | wc -l</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">A one-line command to generate this is:</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 class="diffchange diffchange-inline"> $ MAPPED=$(grep -v "AlignmentBlock" file.mrf | grep -v "#" </ins>| wc -l<ins class="diffchange diffchange-inline">); printf "Mapped_reads\t%d\n" $MAPPED > file.meta</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></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>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=1106&oldid=prevAsboner: /* gfr2bpJunctions */2011-04-05T18:06:02Z<p><span class="autocomment">gfr2bpJunctions</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 18:06, 5 April 2011</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 328:</td>
<td colspan="2" class="diff-lineno">Line 328:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Usage''':</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Usage''':</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> gfr2bpJunctions <file.gfr> <tileSize> <sizeFlankingRegion> <del class="diffchange diffchange-inline">[</del>minDASPER<del class="diffchange diffchange-inline">]</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> gfr2bpJunctions <file.gfr> <tileSize> <sizeFlankingRegion> <ins class="diffchange diffchange-inline"><</ins>minDASPER<ins class="diffchange diffchange-inline">></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>* Input: file.gfr - [[#Gene_Fusion_Report_(GFR)|GFR]] file (not from STDIN)</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Input: file.gfr - [[#Gene_Fusion_Report_(GFR)|GFR]] file (not from STDIN)</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 337:</td>
<td colspan="2" class="diff-lineno">Line 337:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** tileSize: the number of nucleotides in each tile. For example, a 50nt read may be aligned to a 80nt junction, thus tileSize would be 40. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** tileSize: the number of nucleotides in each tile. For example, a 50nt read may be aligned to a 80nt junction, thus tileSize would be 40. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** sizeFlankingRegions: the size, in nucleotides, of the flanking region around the exons.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** sizeFlankingRegions: the size, in nucleotides, of the flanking region around the exons.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;">* Optional parameters:</del></div></td><td colspan="2"> </td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** minDASPER: the minimum DASPER values for which the breakpoint analysis is performed.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** minDASPER: the minimum DASPER values for which the breakpoint analysis is performed.</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>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=837&oldid=prevAsboner: /* geneFusions */2011-02-17T11:20:06Z<p><span class="autocomment">geneFusions</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 11:20, 17 February 2011</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 66:</td>
<td colspan="2" class="diff-lineno">Line 66:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** none</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>** none</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Note''': sample.mrf must include the sequences of the reads. </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Note''': sample.mrf must include the sequences of the reads. </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;"><center>[[#top|Top]]</center></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;">==== gfrClassify ==== </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;">gfrClassify assign each fusion candidate to a specify category: inter-, intra-chromosomal, read-through, or cis. Please see the [http://dx.doi.org/10.1186/gb-2010-11-10-r104 publication] for a description of these classes. </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;">'''Usage''':</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;"> gfrClassify < fileIN.gfr > fileOUT.gfr</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;">* Inputs: Takes a [[#Gene_Fusion_Report_(GFR)|GFR]] file from STDIN</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;">* Outputs: Reports a [[#Gene_Fusion_Report_(GFR)|GFR]] to STDOUT</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><center>[[#top|Top]]</center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td></tr>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=833&oldid=prevAsboner: /* gfr2images */2011-02-16T11:15:53Z<p><span class="autocomment">gfr2images</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 11:15, 16 February 2011</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 421:</td>
<td colspan="2" class="diff-lineno">Line 421:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> gfr2images < fileIN.gfr</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div> gfr2images < fileIN.gfr</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 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-requisite: the pairCount column should be present in the [[#Gene_Fusion_Report_(GFR)|GFR]] file. [[#gfrCountPairTypes|gfrCountPairTypes]] should be executed first.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Inputs: [[#Gene_Fusion_Report_(GFR)|GFR]] from STDIN</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Inputs: [[#Gene_Fusion_Report_(GFR)|GFR]] from STDIN</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Outputs: JPEG images labeled SampleID_0000#.jpg, where '''SampleID''' is the unique identification of the fusion candidate present in the [[#Gene_Fusion_Report_(GFR)|GFR]] file.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>* Outputs: JPEG images labeled SampleID_0000#.jpg, where '''SampleID''' is the unique identification of the fusion candidate present in the [[#Gene_Fusion_Report_(GFR)|GFR]] file.</div></td></tr>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=830&oldid=prevAsboner: /* Gene Fusion Report (GFR) */2011-02-03T22:43:55Z<p><span class="autocomment">Gene Fusion Report (GFR)</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 22:43, 3 February 2011</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Gene Fusion Report (GFR)===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Gene Fusion Report (GFR)===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># the ID of the fusion candidate (''<del class="diffchange diffchange-inline">ID</del>''): typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># the ID of the fusion candidate (''<ins class="diffchange diffchange-inline">id</ins>''): typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># ''SPER'', ''DASPER'' and ''RESPER'': scoring of the fusion candidate;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># ''SPER'', ''DASPER'' and ''RESPER'': scoring of the fusion candidate;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Number of inter-transcript reads (''numInter''), i.e. the number of pairs having the ends mapped to the two genes;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Number of inter-transcript reads (''numInter''), i.e. the number of pairs having the ends mapped to the two genes;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we <del class="diffchange diffchange-inline">computed </del>the p-value for both directions: AB (where gene A is upstream of gene B - ''pValueAB'') and BA (where gene B is upstream of gene A -- ''pValueBA'');</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we <ins class="diffchange diffchange-inline">compute </ins>the p-value for both directions: AB (where gene A is upstream of gene B - ''pValueAB'') and BA (where gene B is upstream of gene A -- ''pValueBA'');</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Mean insert-size value of the minimal fusion transcript fragment. As before for the p-values, we compute both ''interMeanAB'' <del class="diffchange diffchange-inline">and </del>''interMeanBA'';</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Mean insert-size value of the minimal fusion transcript fragment. As before for the p-values, we compute both <ins class="diffchange diffchange-inline">AB and BA versions (</ins>''interMeanAB''<ins class="diffchange diffchange-inline">, </ins>''interMeanBA''<ins class="diffchange diffchange-inline">)</ins>;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Number of intra-transcript reads for gene A (''numIntra1'') and gene B (''numIntra2''), respectively, i.e the number of pairs where both ends map to the same gene;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Number of intra-transcript reads for gene A (''numIntra1'') and gene B (''numIntra2''), respectively, i.e the number of pairs where both ends map to the same gene;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># The type of the fusion (''fusionType''): cis, when both genes are on the same chromosome, or trans, otherwise;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># The type of the fusion (''fusionType''): cis, when both genes are on the same chromosome, or trans, otherwise;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Name(s) of the transcripts (''nameTranscript''): all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '|';</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Name(s) of the transcripts (''nameTranscript''): all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '|';</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Chromosome of the genes (''chromosomeTranscript'';</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Chromosome of the genes (''chromosomeTranscript''<ins class="diffchange diffchange-inline">)</ins>;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Strand information (''strandTranscript'');</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Strand information (''strandTranscript'');</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Start and end coordinates of the longest transcript for both genes (''startTranscript'', ''endTranscript'');</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Start and end coordinates of the longest transcript for both genes (''startTranscript'', ''endTranscript'');</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Number of exons in the composite model for both genes (''numExonTranscript'');</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Number of exons in the composite model for both genes (''numExonTranscript'');</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Coordinates of the exons in the composite model: each exon is separated by the pipe symbol '|' and start and end coordinates are comma-separated;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Coordinates of the exons in the composite model <ins class="diffchange diffchange-inline">(''exonCoordinatesTranscript'')</ins>: each exon is separated by the pipe symbol '|' and start and end coordinates are comma-separated;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># interReads: the pair-read type, as well as the exons and the coordinates of the reads joining the two genes. Pair-type, exon number, start and end coordinates are reported as a comma-separated list, with the pipe symbol '|' separating the different pairs. The pair-reads type encodes the different possibilities two reads can be classified to in terms of the gene annotation set:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># interReads: the pair-read type, as well as the exons and the coordinates of the reads joining the two genes. Pair-type, exon number, start and end coordinates are reported as a comma-separated list, with the pipe symbol '|' separating the different pairs. The pair-reads type encodes the different possibilities two reads can be classified to in terms of the gene annotation set:</div></td></tr>
<tr><td colspan="2" class="diff-lineno">Line 34:</td>
<td colspan="2" class="diff-lineno">Line 34:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Reads of the transcripts: the actual sequence of all the inter-reads.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Reads of the transcripts: the actual sequence of all the inter-reads.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Pair-count: a summary of the number of reads for each category and joined exons (see interReads for the category definition). The field reports the pair-reads type, the number of reads, the two exons that are joined by the pair as a comma-separated list. The different pair types are separated by the pipe "|" symbol.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Pair-count: a summary of the number of reads for each category and joined exons (see interReads for the category definition). The field reports the pair-reads type, the number of reads, the two exons that are joined by the pair as a comma-separated list. The different pair types are separated by the pipe "|" symbol.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols and descriptions from the UCSC knownGene annotation set.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols <ins class="diffchange diffchange-inline">(''geneSymbolTranscript'') </ins>and descriptions <ins class="diffchange diffchange-inline">(''descriptionTranscript'') </ins>from the UCSC knownGene annotation set.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></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>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=829&oldid=prevAsboner: /* Gene Fusion Report (GFR) */2011-02-03T22:35:55Z<p><span class="autocomment">Gene Fusion Report (GFR)</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 22:35, 3 February 2011</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 8:</td>
<td colspan="2" class="diff-lineno">Line 8:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Gene Fusion Report (GFR)===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Gene Fusion Report (GFR)===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This file format defines the relevant information for each fusion transcript candidate. The rationale is that different filters can be applied to exclude “false positives” artificial fusions starting from an initial set. We also provide a parser that interprets this format allowing the user to propagate easily any changes to this format. For a given fusion candidate, involving gene A and gene B, the basic GFR format requires the following fields:</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># <del class="diffchange diffchange-inline">ID: </del>the ID of the fusion candidate: typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># the ID of the fusion candidate <ins class="diffchange diffchange-inline">(''ID'')</ins>: typically it contains the sample name and a unique number separated by an underscore. The number is padded with zeros for consistency;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># SPER, DASPER and RESPER: scoring of the fusion candidate;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># <ins class="diffchange diffchange-inline">''</ins>SPER<ins class="diffchange diffchange-inline">''</ins>, <ins class="diffchange diffchange-inline">''</ins>DASPER<ins class="diffchange diffchange-inline">'' </ins>and <ins class="diffchange diffchange-inline">''</ins>RESPER<ins class="diffchange diffchange-inline">''</ins>: scoring of the fusion candidate;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Number of inter-transcript reads, i.e. the number of pairs having the ends mapped to the two <del class="diffchange diffchange-inline"> </del>genes;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Number of inter-transcript reads <ins class="diffchange diffchange-inline">(''numInter'')</ins>, i.e. the number of pairs having the ends mapped to the two genes;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we computed the p-value for both directions: AB (where gene A is upstream of gene B) and BA (where gene B is upstream of gene A);</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># P-value of the insert size distribution analysis for the fusion transcript. Since we do not know the actual composition of the fusion transcript, we computed the p-value for both directions: AB (where gene A is upstream of gene B <ins class="diffchange diffchange-inline">- ''pValueAB''</ins>) and BA (where gene B is upstream of gene A <ins class="diffchange diffchange-inline">-- ''pValueBA''</ins>)<ins class="diffchange diffchange-inline">;</ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Number of intra-transcript reads for gene A and gene B, respectively, i.e the number of pairs where both ends map to the same gene;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"># Mean insert-size value of the minimal fusion transcript fragment. As before for the p-values, we compute both ''interMeanAB'' and ''interMeanBA''</ins>;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># The type of the fusion: cis, when both genes are on the same chromosome, or trans, otherwise;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Number of intra-transcript reads for gene A <ins class="diffchange diffchange-inline">(''numIntra1'') </ins>and gene B <ins class="diffchange diffchange-inline">(''numIntra2'')</ins>, respectively, i.e the number of pairs where both ends map to the same gene;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Name(s) of the transcripts: all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '|';</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># The type of the fusion <ins class="diffchange diffchange-inline">(''fusionType'')</ins>: cis, when both genes are on the same chromosome, or trans, otherwise;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Chromosome of the genes;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Name(s) of the transcripts <ins class="diffchange diffchange-inline">(''nameTranscript'')</ins>: all the UCSC gene IDs of the isoforms of each gene in the annotation separated by the pipe symbol '|';</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Strand information;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Chromosome of the genes <ins class="diffchange diffchange-inline">(''chromosomeTranscript''</ins>;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Start and end coordinates of the longest transcript for both genes;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># <ins class="diffchange diffchange-inline"> </ins>Strand information <ins class="diffchange diffchange-inline">(''strandTranscript'')</ins>;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># Number of exons in the composite model for both genes;</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Start and end coordinates of the longest transcript for both genes <ins class="diffchange diffchange-inline">(''startTranscript'', ''endTranscript'')</ins>;</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># Number of exons in the composite model for both genes <ins class="diffchange diffchange-inline">(''numExonTranscript'')</ins>;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Coordinates of the exons in the composite model: each exon is separated by the pipe symbol '|' and start and end coordinates are comma-separated;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Coordinates of the exons in the composite model: each exon is separated by the pipe symbol '|' and start and end coordinates are comma-separated;</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Exon-pair count: it describes which elements are connected and corresponding number of inter-transcript reads;</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div># <del class="diffchange diffchange-inline">Inter-reads</del>: the <del class="diffchange diffchange-inline">exon </del>and the coordinates of the reads <del class="diffchange diffchange-inline">that join </del>the two genes. <del class="diffchange diffchange-inline">Exon </del>number, start and end coordinates are reported as comma-separated, with the pipe symbol '|' separating the different pairs<del class="diffchange diffchange-inline">;</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div># <ins class="diffchange diffchange-inline">interReads</ins>: the <ins class="diffchange diffchange-inline">pair-read type, as well as the exons </ins>and the coordinates of the reads <ins class="diffchange diffchange-inline">joining </ins>the two genes. <ins class="diffchange diffchange-inline">Pair-type, exon </ins>number, start and end coordinates are reported as <ins class="diffchange diffchange-inline">a </ins>comma-separated <ins class="diffchange diffchange-inline">list</ins>, with the pipe symbol '|' separating the different pairs<ins class="diffchange diffchange-inline">. The pair-reads type encodes the different possibilities two reads can be classified to in terms of the gene annotation set:</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 class="diffchange diffchange-inline">#* 1 : exon-exon</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 class="diffchange diffchange-inline">#* 2 : exon-intron</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 class="diffchange diffchange-inline">#* 3 : intron-exon</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 class="diffchange diffchange-inline">#* 4 : intron-intron</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 class="diffchange diffchange-inline">#* 5 : intron-boundary</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 class="diffchange diffchange-inline">#* 6 : exon-boundary</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 class="diffchange diffchange-inline">#* 7 : boundary-exon</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 class="diffchange diffchange-inline">#* 8 : boundary-intron</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 class="diffchange diffchange-inline">#* 9 : boundary-boundary</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Reads of the transcripts: the actual sequence of all the inter-reads.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div># Reads of the transcripts: the actual sequence of all the inter-reads.</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;"># Pair-count: a summary of the number of reads for each category and joined exons (see interReads for the category definition). The field reports the pair-reads type, the number of reads, the two exons that are joined by the pair as a comma-separated list. The different pair types are separated by the pipe "|" symbol.</ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols and descriptions from the UCSC knownGene annotation set.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The GFR format can include additional optional information computed in the subsequent processing. For example, it is possible to add gene symbols and descriptions from the UCSC knownGene annotation set.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td></tr>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=738&oldid=prevAsboner: /* export2mrf */2010-12-03T06:45:55Z<p><span class="autocomment">export2mrf</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 06:45, 3 December 2010</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 458:</td>
<td colspan="2" class="diff-lineno">Line 458:</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>It generates an MRF file from the export files of a Genome Analyzer II run.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It generates an MRF file from the export files of a Genome Analyzer II run.</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Usage''':</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Usage''':</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 colspan="2" class="diff-lineno">Line 472:</td>
<td colspan="2" class="diff-lineno">Line 473:</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><center>[[#top|Top]]</center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </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>==== gfrAddInfo ==== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrAddInfo ==== </div></td></tr>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=737&oldid=prevAsboner: /* gfrAddInfo */2010-12-03T06:45:42Z<p><span class="autocomment">gfrAddInfo</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 06:45, 3 December 2010</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 477:</td>
<td colspan="2" class="diff-lineno">Line 477:</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>It includes additional information about the fusion transcript candidates such as gene symbols and gene description. This is a pre-requisite for [[#gfrBlackListFilter|gfrBlackListFilter]] and [[#gfrAnnotationConsistencyFilter|gfrAnnotationConsistencyFilter]].</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It includes additional information about the fusion transcript candidates such as gene symbols and gene description. This is a pre-requisite for [[#gfrBlackListFilter|gfrBlackListFilter]] and [[#gfrAnnotationConsistencyFilter|gfrAnnotationConsistencyFilter]].</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Usage''':</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Usage''':</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>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=735&oldid=prevAsboner: /* Mis-alignment filters */2010-12-03T06:43:05Z<p><span class="autocomment">Mis-alignment filters</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 06:43, 3 December 2010</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 60:</td>
<td colspan="2" class="diff-lineno">Line 60:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Filtration cascade module==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Filtration cascade module==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Mis-alignment filters===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Mis-alignment filters===</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;">----</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrLargeScaleHomologyFilter ==== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrLargeScaleHomologyFilter ==== </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It removes potential fusion transcript candidates if the two genes are paralogs. It uses [http://www.treefam.org/ TreeFam] to establish is two genes have similar sequences.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It removes potential fusion transcript candidates if the two genes are paralogs. It uses [http://www.treefam.org/ TreeFam] to establish is two genes have similar sequences.</div></td></tr>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asbonerhttp://info.gersteinlab.org/index.php?title=FusionSeq_List_of_programs&diff=734&oldid=prevAsboner: /* Random pairing of transcript fragments */2010-12-03T06:42:35Z<p><span class="autocomment">Random pairing of transcript fragments</span></p>
<table style="background-color: white; color:black;">
<col class='diff-marker' />
<col class='diff-content' />
<col class='diff-marker' />
<col class='diff-content' />
<tr valign='top'>
<td colspan='2' style="background-color: white; color:black;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black;">Revision as of 06:42, 3 December 2010</td>
</tr>
<tr><td colspan="2" class="diff-lineno">Line 101:</td>
<td colspan="2" class="diff-lineno">Line 101:</td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><center>[[#top|Top]]</center></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>==Random pairing of transcript fragments==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">=</ins>==Random pairing of transcript fragments==<ins class="diffchange diffchange-inline">=</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">----</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrAbnormalInsertSizeFilter ==== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrAbnormalInsertSizeFilter ==== </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 colspan="2" class="diff-lineno">Line 118:</td>
<td colspan="2" class="diff-lineno">Line 121:</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>===Combination of mis-alignment and random pairing===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Combination of mis-alignment and random pairing===</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;">----</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrRibosomalFilter ==== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrRibosomalFilter ==== </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 colspan="2" class="diff-lineno">Line 145:</td>
<td colspan="2" class="diff-lineno">Line 151:</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>===Other filters===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Other filters===</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;">----</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrPCRFilter ==== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrPCRFilter ==== </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 colspan="2" class="diff-lineno">Line 241:</td>
<td colspan="2" class="diff-lineno">Line 250:</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>===Scoring the candidates===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>===Scoring the candidates===</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;">----</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 class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrConfidenceValues ==== </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== gfrConfidenceValues ==== </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>
<!-- diff generator: internal 2024-03-29 08:11:15 -->
</table>Asboner