https://www.jstacs.de/index.php?title=CRISPRer&feed=atom&action=historyCRISPRer - Revision history2024-03-28T21:46:21ZRevision history for this page on the wikiMediaWiki 1.38.2https://www.jstacs.de/index.php?title=CRISPRer&diff=648&oldid=prevGrau: /* Running the command line application */2013-07-17T20:46:54Z<p><span dir="auto"><span class="autocomment">Running the command line application</span></span></p>
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<td colspan="2" style="background-color: #fff; color: #202122; text-align: center;">Revision as of 21:46, 17 July 2013</td>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For instance, using the input parameters</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>For instance, using the input parameters</div></td></tr>
<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> <code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa length=20 seed=12</code></div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div> <code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa length=20 seed=12</code></div></td></tr>
<tr><td class="diff-marker" data-marker="−"></td><td style="color: #202122; 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>CRISPRer searches for protospacers of length 20 with unique seeds of length 12 in the genome given in the FastA file <code>path/to/genome.fa<del style="font-weight: bold; text-decoration: none;">} </del>using PAM <code>NGG<del style="font-weight: bold; text-decoration: none;">} </del>and appends the sequence matching the PAM to the output sequences.</div></td><td class="diff-marker" data-marker="+"></td><td style="color: #202122; 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>CRISPRer searches for protospacers of length 20 with unique seeds of length 12 in the genome given in the FastA file <code>path/to/genome.fa<ins style="font-weight: bold; text-decoration: none;"></code> </ins>using PAM <code>NGG<ins style="font-weight: bold; text-decoration: none;"></code> </ins>and appends the sequence matching the PAM to the output sequences.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If the input parameters are</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>If the input parameters are</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>CRISPRer assesses the protospacer sequences given in the FastA file <code>path/to/protospacers.fa</code> using PAM <code>NGG</code> and seed length 10.</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>CRISPRer assesses the protospacer sequences given in the FastA file <code>path/to/protospacers.fa</code> using PAM <code>NGG</code> and seed length 10.</div></td></tr>
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<tr><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Installing the web-application ==</div></td><td class="diff-marker"></td><td style="background-color: #f8f9fa; color: #202122; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #eaecf0; vertical-align: top; white-space: pre-wrap;"><div>== Installing the web-application ==</div></td></tr>
</table>Grauhttps://www.jstacs.de/index.php?title=CRISPRer&diff=647&oldid=prevGrau: Created page with "by Jan Grau, Jens Boch, and Stefan Posch. CRISPRer is a tool for genome-wide selection and assessment of CRISPR/Cas protospacers. CRISPRer offers three distinct tasks. First, CR..."2013-07-17T20:46:07Z<p>Created page with "by Jan Grau, Jens Boch, and Stefan Posch. CRISPRer is a tool for genome-wide selection and assessment of CRISPR/Cas protospacers. CRISPRer offers three distinct tasks. First, CR..."</p>
<p><b>New page</b></p><div>by Jan Grau, Jens Boch, and Stefan Posch.<br />
<br />
CRISPRer is a tool for genome-wide selection and assessment of CRISPR/Cas protospacers. CRISPRer offers three distinct tasks.<br />
First, CRISPRer may search for protospacers with unique seed sequences, i.e., with seed sequences which occur only once in a given input genome.<br />
Second, it may search for seed sequences that are orthogonal to the input genome, i.e., which do not occur in the given input genome.<br />
Third, it may assess a set of user-provided protospacers by collecting several statistics about genome-wide perfect and imperfect matches to their seed sequences.<br />
<br />
We provide CRISPRer as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program.<br />
<br />
== CRISPRer web-server ==<br />
CRISPRer is available as a public web-server at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].<br />
<br />
== Download ==<br />
<br />
CRISPRer is implemented in Java using Jstacs. You can download the command line application as a [http://www.jstacs.de/download.php?which=CRISPRer Jar].<br />
In addition, we provide the [http://www.jstacs.de/download.php?which=CRISPRerWeb Jar of the Galaxy web-application] for installing it in your local [http://getgalaxy.org Galaxy] server.<br />
<br />
CRISPRer will be part of the next public release of the Jstacs library. As (future) part of Jstacs, CRISPRer will be released under GPL 3.<br />
<br />
== Running the command line application ==<br />
<br />
For running the command line application, Java v1.6 or later is required.<br />
<br />
The arguments of the command line application have the following meaning:<br />
<br />
<table border=0 cellpadding=10 align="center"><br />
<tr><br />
<td>name</td><br />
<td>comment</td><br />
<td>type</td><br />
</tr><br />
<tr><td colspan=3><hr></td></tr><br />
<tr><br />
<td><font color="green">input</font></td><br />
<td>Input data (The genome for that CRISPR/Cas protospacers/seeds are selected, FastA format)</td><br />
<td>String</td><br />
</tr><tr><br />
<td><font color="green">length</font></td><br />
<td>Length (The length of the protospacer, default = 20)</td><br />
<td>Integer</td><br />
</tr><tr><br />
<td><font color="green">seed</font></td><br />
<td>Seed length (The length of the seed at the 3' end of the protospacer, valid range = [1, 13], default = 12)</td><br />
<td>Integer</td><br />
</tr><tr><br />
<td><font color="green">pam</font></td><br />
<td>PAM (The PAM pattern, all IUPAC DNA symbols allowed, default = NGG)</td><br />
<td>String</td><br />
</tr><tr><br />
<td><font color="green">filter</font></td><br />
<td>Chromosomal locations (The chromosomal locations for which to filter the reported protospacers. Enter different location separated by semicolons. Ignored if parameter proto set., OPTIONAL)</td><br />
<td>String</td><br />
</tr><tr><br />
<td><font color="green">proto</font></td><br />
<td>Protospacers (Protospacers (without PAM sequence) to assess genome-wide, FastA format, OPTIONAL)</td><br />
<td>String</td><br />
</tr><tr><br />
<td><font color="green">unique</font></td><br />
<td>Unique seeds (If true, CRISPRer searches for protospacers with unique seeds. Otherwise, it searches for orthogonal seeds., default = true)</td><br />
<td>Boolean</td><br />
</tr><tr><br />
<td><font color="green">include</font></td><br />
<td>Include PAM (Include sequence matching PAM pattern in output, default = true)</td><br />
<td>Boolean</td><br />
</tr><tr><br />
<td><font color="green">prefix</font></td><br />
<td>Output prefix (Common prefix of all output files, may include path, default = ./CRISPRer)</td><br />
<td>String</td><br />
</tr><tr><br />
<td><font color="green">gff2</font></td><br />
<td>Use GFF2 (Use GFF2 output format instead of GFF3, default = false)</td><br />
<td>Boolean</td><br />
</tr><br />
</table><br />
<br />
For instance, using the input parameters<br />
<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa length=20 seed=12</code><br />
CRISPRer searches for protospacers of length 20 with unique seeds of length 12 in the genome given in the FastA file <code>path/to/genome.fa} using PAM <code>NGG} and appends the sequence matching the PAM to the output sequences.<br />
<br />
If the input parameters are<br />
<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa seed=10 pam=NCC unique=false include=false</code><br />
CRISPRer searches for orthogonal seeds of length 10 using PAM <code>NCC</code>, instead.<br />
<br />
Finally, if the input parameters are<br />
<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa seed=10 pam=NGG proto=path/to/protospacers.fa</code><br />
CRISPRer assesses the protospacer sequences given in the FastA file <code>path/to/protospacers.fa</code> using PAM <code>NGG</code> and seed length 10.<br />
<br />
<br />
== Installing the web-application ==<br />
<br />
The command-line program behind the web-application is a Jar as well, so Java is required on the server running Galaxy.<br />
To install this command line program in Galaxy, copy it to the desired destination in the Galaxy <code>tools</code> directory.<br />
<br />
The command line application writes its Galaxy tool definition file itself. If you are in the directory containing the command-line program for Galaxy, you can create the tool definition file by calling<br />
<code>java -jar CRISPRerWeb --create CRISPRerWeb.xml</code><br />
<br />
Afterwards, this directory contains the tool definition file <code>CRISPRerWeb.xml</code>. Now you can register CRISPRer in the Galaxy <code>tool_conf.xml</code> file. For details, see the [http://wiki.g2.bx.psu.edu/Admin/Tools/Add%20Tool%20Tutorial Galaxy tutorial for adding new tools].</div>Grau