Version Differences for Manual2
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(→Test-mammer)
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(→Test-mammer)
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| = Test-mammer = | = Test-mammer = | ||
| + | <ul><li><strong>Prepair datasets:</strong> the contigs which generate from different softwares you would like to integrate</li></ul><blockquote><p>Ecoli</p></blockquote><ul><li><strong>Convert the format and ID of your datasets:</strong><br /></li></ul><blockquote><p> The content of the configuration file (Merge.config):</p></blockquote> | ||
| - | <ul><li><strong>Data Set:</strong></li></ul><blockquote><p>Ecoli</p></blockquote><ul><li><strong>Merge Contigs:</strong><br /></li></ul><blockquote><p>The content of the configuration file:</p></blockquote> | + | {| width="457" border="1" |
| - | {| width="699" border="1" | + | | width="467" height="152" align="left" bgcolor="#66CCFF" | <blockquote><pre>count=5 |
| - | | width="689" height="152" align="left" bgcolor="#66CCFF" | <blockquote><pre>count=5 | + | data=Abyss_contigs.fa,title=Abyss |
| - | data=Abyss_contigs.fa,title=Abyss <font color="#FF0000">設定hyperlink到example file,方便直接下載</font> | ||
| data=Edena_contigs.fa,title=Edena | data=Edena_contigs.fa,title=Edena | ||
| data=SOAPdenovo_contigs.fa,title=SOAP | data=SOAPdenovo_contigs.fa,title=SOAP | ||
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| data=Velvet_contigs.fa,title=Velvet | data=Velvet_contigs.fa,title=Velvet | ||
| Master_file=Contigs.fa</pre></blockquote> | Master_file=Contigs.fa</pre></blockquote> | ||
| - | |}<ul><li><strong>Command:</strong><br /></li></ul><blockquote><p>./Merge.py myconfig</p></blockquote><p><br /></p><ul><li><strong>Start to integrate:</strong><br /></li></ul><blockquote><p>The content of the configuration file:</p></blockquote> | + | |}<ul><li><strong>Command:</strong><br /></li></ul><blockquote><p><span class="red">>python </span> Merge.py Merge.config</p></blockquote><ul><li><strong>Start to integrate contigs:</strong><br /></li></ul><blockquote><p>The content of the configuration file (CISA.config):</p></blockquote> |
| {| width="467" border="1" | {| width="467" border="1" | ||
| | width="457" height="152" align="left" bgcolor="#66CCFF" | <blockquote><pre> | | width="457" height="152" align="left" bgcolor="#66CCFF" | <blockquote><pre> | ||
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| makeblastdb=path/makeblastdb | makeblastdb=path/makeblastdb | ||
| blastn=path/blastn</pre></blockquote> | blastn=path/blastn</pre></blockquote> | ||
| - | |}<blockquote><p>4626205 which is the longest whole genome between different result from 5 assemblers is set into genome variable. <br /></p></blockquote><ul><li><strong>Command:</strong><br /></li></ul><p>./CISA.py myconfig</p> | + | |}<blockquote><p>4626205 which is the longest whole genome between different result from 5 assemblers is set into genome variable. <br /></p></blockquote><ul><li><strong>Command:</strong><br /></li></ul><blockquote><p><span class="red">>python </span> CISA.py CISA.config</p></blockquote> |