https://sourceforge.net/p/imrep/wiki/Running%2520ImReP/Recent changes to Running ImRePenFri, 18 Nov 2016 07:29:37 -0000https://sourceforge.net/p/imrep/wiki/Running%2520ImReP/<div class="markdown_content"><h2 id="imrep-help-message">ImReP help message</h2> <p>In order to see ImReP help message, invoke</p> <div class="codehilite"><pre><span class="nv">$ </span>python imrep.py -h </pre></div> <p>from the command line.</p> <h2 id="necessary-parameters">Necessary parameters</h2> <ul> <li> <p>reads_fastq - file with RNA-Seq or TCR-(BCR-)-Seq reads in .fastq format. If the reads are paired, then you must ensure that they are stored in one file.</p> </li> <li> <p>output_clones - output file.</p> </li> </ul> <h2 id="optional-parameters">Optional parameters</h2> <ul> <li> <p>-o OVERLAPLEN, --overlapLen OVERLAPLEN - the minimal length to consider between reads overlapping with a V gene and reads overlapping with a J gene. Default value is 10 amino acids. </p> </li> <li> <p>--noOverlapStep - a binary flag used in case if the user does not want to run the second stage of the ImReP assembly.</p> </li> <li> <p>-t CASTTHRESHOLD - a custom parameter which controls the stringency of CDR3 clustering. Current version of ImReP uses <a class="" href="http://online.liebertpub.com/doi/abs/10.1089/106652799318274" rel="nofollow">CAST</a> clustering algorithm for building clonotypes. The default value is 0.2</p> </li> <li> <p>-c CHAINS, --chains CHAINS - comma separated value of chains to search for. The default value is IGH,IGK,IGL,TRA,TRB,TRD,TRG.</p> </li> </ul></div>Igor MandricFri, 18 Nov 2016 07:29:37 -0000https://sourceforge.netd859d980b43b454b86fbbe4b53b288a31f0138c1