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read-tide-index.html
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<!DOCTYPE html>
<html>
<head>
<title>read-tide-index</title>
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<div id="content" class="autogenerated">
<!-- START CONTENT -->
<h1>read-tide-index</h1>
<h2>Usage:</h2>
<p><code>crux read-tide-index [options] <tide database></code></p>
<h2>Description:</h2>
Reads an index generated by tide-index and outputs information about the peptides it contains.
<h2>Input:</h2>
<ul>
<li><code>tide database</code> – Either a FASTA file or a directory containing a database index created by a previous run of crux tide-index.</li>
</ul>
<h2>Output:</h2>
<p>The program writes files to the folder <code>crux-output</code> by default. The name of the output folder can be set by the user using the <code>--output-dir</code> option. The following files will be created:
<ul>
<li><code>read-tide-index.peptides.txt</code> – a tab-delimited file containing two columns with headers: the peptide, and a semicolon-delimited list of IDs of the proteins that peptide occurs in.</li>
<li><code>read-tide-index.params.txt</code> – a file containing the name and value of all parameters/options for the current operation. Not all parameters in the file may have been used in the operation. The resulting file can be used with the --parameter-file option for other crux programs.</li>
<li><code>read-tide-index.log.txt</code> – a log file containing a copy of all messages that were printed to the screen during execution.</li>
</ul>
<h2>Options:</h2>
<ul style="list-style-type: none;">
<li class="nobullet">
<p>This command does not support any optional parameters.</p>
</li>
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The original version of Crux was written by Chris Park and Aaron Klammer
under the supervision
of <a href="http://www.gs.washington.edu/faculty/maccoss.htm">Prof. Michael
MacCoss</a>
and <a href="http://noble.gs.washington.edu/~noble">Prof. William
Stafford Noble</a> in the Department of Genome Sciences at the
University of Washington, Seattle. Website by <a href="http://www.yuvalboss.com/">Yuval Boss</a>
<br />The complete list of contributors
can be found <a href="../contributors.html">here</a>.
<br />
<br />
Maintenance and development of Crux is funded by the <a href="https://www.nih.gov/">National Institutes of Health</a> awards R01 GM096306 and P41 GM103533.
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