Grau: /* Running the command line application */

2013-07-17T20:46:54Z

Running the command line application

← Older revision		Revision as of 20:46, 17 July 2013
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	For instance, using the input parameters		For instance, using the input parameters
	<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa length=20 seed=12</code>		<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa length=20 seed=12</code>
	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.		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</code> using PAM <code>NGG</code> and appends the sequence matching the PAM to the output sequences.

	If the input parameters are		If the input parameters are
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	<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa seed=10 pam=NGG proto=path/to/protospacers.fa</code>		<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa seed=10 pam=NGG proto=path/to/protospacers.fa</code>
	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.		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.


	== Installing the web-application ==		== Installing the web-application ==

Grau: 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

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..."

New page

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, CRISPRer may search for protospacers with unique seed sequences, i.e., with seed sequences which occur only once in a given input genome.
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.
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.

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.

== CRISPRer web-server ==
CRISPRer is available as a public web-server at [http://galaxy.informatik.uni-halle.de galaxy.informatik.uni-halle.de].

== Download ==

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].
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.

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.

== Running the command line application ==

For running the command line application, Java v1.6 or later is required.

The arguments of the command line application have the following meaning:

<table border=0 cellpadding=10 align="center">
<tr>
<td>name</td>
<td>comment</td>
<td>type</td>
</tr>
<tr><td colspan=3><hr></td></tr>
<tr>
<td>input</td>
<td>Input data (The genome for that CRISPR/Cas protospacers/seeds are selected, FastA format)</td>
<td>String</td>
</tr><tr>
<td>length</td>
<td>Length (The length of the protospacer, default = 20)</td>
<td>Integer</td>
</tr><tr>
<td>seed</td>
<td>Seed length (The length of the seed at the 3' end of the protospacer, valid range = [1, 13], default = 12)</td>
<td>Integer</td>
</tr><tr>
<td>pam</td>
<td>PAM (The PAM pattern, all IUPAC DNA symbols allowed, default = NGG)</td>
<td>String</td>
</tr><tr>
<td>filter</td>
<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>
<td>String</td>
</tr><tr>
<td>proto</td>
<td>Protospacers (Protospacers (without PAM sequence) to assess genome-wide, FastA format, OPTIONAL)</td>
<td>String</td>
</tr><tr>
<td>unique</td>
<td>Unique seeds (If true, CRISPRer searches for protospacers with unique seeds. Otherwise, it searches for orthogonal seeds., default = true)</td>
<td>Boolean</td>
</tr><tr>
<td>include</td>
<td>Include PAM (Include sequence matching PAM pattern in output, default = true)</td>
<td>Boolean</td>
</tr><tr>
<td>prefix</td>
<td>Output prefix (Common prefix of all output files, may include path, default = ./CRISPRer)</td>
<td>String</td>
</tr><tr>
<td>gff2</td>
<td>Use GFF2 (Use GFF2 output format instead of GFF3, default = false)</td>
<td>Boolean</td>
</tr>
</table>

For instance, using the input parameters
<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa length=20 seed=12</code>
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.

If the input parameters are
<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa seed=10 pam=NCC unique=false include=false</code>
CRISPRer searches for orthogonal seeds of length 10 using PAM <code>NCC</code>, instead.

Finally, if the input parameters are
<code>java -Xms512M -Xmx3G -jar CRISPRer.jar input=path/to/genome.fa seed=10 pam=NGG proto=path/to/protospacers.fa</code>
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.

== Installing the web-application ==

The command-line program behind the web-application is a Jar as well, so Java is required on the server running Galaxy.
To install this command line program in Galaxy, copy it to the desired destination in the Galaxy <code>tools</code> directory.

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
<code>java -jar CRISPRerWeb --create CRISPRerWeb.xml</code>

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].

CRISPRer - Revision history

Grau: /* Running the command line application */

Grau: 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..."