http://amos.sourceforge.net/wiki/index.php?action=history&feed=atom&title=Bambus%2FprintScaffBambus/printScaff - Revision history2026-04-30T14:29:09ZRevision history for this page on the wikiMediaWiki 1.23.5http://amos.sourceforge.net/wiki/index.php?title=Bambus/printScaff&diff=309&oldid=prevDmb000006 at 14:57, 7 January 20112011-01-07T14:57:34Z<p></p>
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<td colspan='2' style="background-color: white; color:black; text-align: center;">← Older revision</td>
<td colspan='2' style="background-color: white; color:black; text-align: center;">Revision as of 14:57, 7 January 2011</td>
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<tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>The '''printScaff''' command is a part of the [[Bambus]] pipeline.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>The '''printScaff''' command is a part of the [[<ins class="diffchange diffchange-inline">Bambus Manual|</ins>Bambus]] pipeline.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>PrintScaff requires as inputs the [[Bambus Manual#.evidence.xml|.evidence.xml]] file, the [[Bambus Manual#.out.xml|.out.xml]] file and the [[Bambus Manual#.lib file|.lib]] files produce by Bambus, the minimal invocation being:</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>PrintScaff requires as inputs the [[Bambus Manual#.evidence.xml|.evidence.xml]] file, the [[Bambus Manual#.out.xml|.out.xml]] file and the [[Bambus Manual#.lib file|.lib]] files produce by Bambus, the minimal invocation being:</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* -merge - (default) when the -f option is given, produce a pseudo-molecule for each scaffold by adding 60 N characters between the contigs in the scaffold</div></td><td class='diff-marker'> </td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>* -merge - (default) when the -f option is given, produce a pseudo-molecule for each scaffold by adding 60 N characters between the contigs in the scaffold</div></td></tr>
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</table>Dmb000006http://amos.sourceforge.net/wiki/index.php?title=Bambus/printScaff&diff=308&oldid=prevDmb000006: Fixing 'internal links' to point back at the bambus manual2011-01-07T14:54:28Z<p>Fixing 'internal links' to point back at the bambus manual</p>
<p><b>New page</b></p><div>The '''printScaff''' command is a part of the [[Bambus]] pipeline.<br />
<br />
PrintScaff requires as inputs the [[Bambus Manual#.evidence.xml|.evidence.xml]] file, the [[Bambus Manual#.out.xml|.out.xml]] file and the [[Bambus Manual#.lib file|.lib]] files produce by Bambus, the minimal invocation being:<br />
<br />
printScaff -e test.evidence.xml -s test.out.xml -l test.lib<br />
<br />
<br />
Optionally you may specify the output prefix with option -o (just like in the [[Bambus Manual|Bambus invocation]]). PrintScaff has parameters that control what gets reported, and in what format.<br />
<br />
In the first category you have:<br />
* -dot - produce a .dot file<br />
* -detail - produce a .details file<br />
* -oo - produce a [[Bambus Manual#.oo file|.oo]] file listing all the contigs in each scaffold<br />
* -sum - produce a [[Bambus Manual#.sum file|.sum]] tab delimited list of scaffold stats (#contigs, size, and span)<br />
* -f <fasta_file> - generate a pseudo-molecule for each scaffold using the contig sequences listed in <fasta_file>. Note that the contigs in the scaffold files are names "contig_<id>" while the contigs in the <fasta_file> must simply be called "<id>". Note that this option together with the default -merge option (see below) is meaningless unless you've [[Bambus Manual#Untangling scaffolds|untangled]] the scaffold.<br />
* -phys - create a .phys file listing all "gaps" spanned only by the specified libraries:<br />
<br />
printScaff -e test.evidence.xml -s test.out.xml -l test.lib -phys MUMmer<br />
<br />
will generate a file called test.phys that contains all contig pairs linked by nothing but MUMmer links.<br />
<br />
<br />
In the second category you have:<br />
* -page - produce .dot file formatted for printing on 8.5x11" paper<br />
* -plot - produce .dot file formatted for printing on a plotter (36x48" paper)<br />
* -unused - draw edges corresponding to unused links<br />
* -merge - (default) when the -f option is given, produce a pseudo-molecule for each scaffold by adding 60 N characters between the contigs in the scaffold<br />
* -nomerge - when the -f option is given, create a fasta file containing all contigs in each scaffold in the correct orientation</div>Dmb000006