https://sourceforge.net/p/tuque/wiki/UseTuque/Recent changes to UseTuqueenWed, 10 Apr 2013 17:27:41 -0000https://sourceforge.net/p/tuque/wiki/UseTuque/<div class="markdown_content"><pre>--- v1 +++ v2 @@ -13,8 +13,7 @@ -m The maximum amount of RAM to use, in bytes \[10000000000\] -o Path to a directory where output should be written \[Genome/RNA-Seq\]. It will be created if it does not exist. - -n The number of input reads files \[1\]; if n > 1 these files should be named - Reads_filename.1 through Reads_filename.n + -n The number of input reads files \[1\]; if n > 1 these files should be named Reads_filename.1 through Reads_filename.n Only the genome filename and the reads filename need to be specified; the other parameters have reasonable default values. </pre> </div>Ian ReidWed, 10 Apr 2013 17:27:41 -0000https://sourceforge.netd5f5d8c21ce014a6401dca37a31415ec2aae7311https://sourceforge.net/p/tuque/wiki/UseTuque/<div class="markdown_content"><h1 id="running-the-programs">Running the programs</h1> <h2 id="tuquesplice">tuqueSplice</h2> <p>tuqueSplice will find the splice junctions in a set of RNA-Seq reads and map the reads to a genome.</p> <p><strong>Command line:</strong> tuqueSplice -g Genome_sequence_filename [-j Predicted.juncs] [-m Memory limit] [-o Output directory] [-n Number of input files] [-c Config file path] Reads_filename<br /> Parameters:<br /> -c Path to configuration file [tuque/tuque.cfg]<br /> -g The name of a fasta file containing the genome sequence to be mapped against. Required.<br /> -j Name of a file containing predicted splice junctions in .juncs format [None]<br /> -m The maximum amount of RAM to use, in bytes [10000000000]<br /> -o Path to a directory where output should be written [Genome/RNA-Seq]. It will be created if it does<br /> not exist.<br /> -n The number of input reads files [1]; if n &gt; 1 these files should be named<br /> Reads_filename.1 through Reads_filename.n</p> <p>Only the genome filename and the reads filename need to be specified; the other parameters have reasonable default<br /> values.</p> <p><strong>Outputs:</strong><br /> Filtered splice junction locations in classified.juncs<br /> Read mappings in tuque_hits.bam<br /> Coverage depths in tuque.coverage.wig.gz<br /> tuqueSplice.log contains a complete record of the run and bowtie.log contains read mapping statistics.</p> <h2 id="tuquesplice_ps">tuqueSplice_ps</h2> <p>tuqueSplice_ps is a variant of tuqueSplice that is more efficient in genomes with numerous small scaffolds or contigs.</p> <p><strong>Command line:</strong> tuqueSplice -g Genome_sequence_filename [-j Predicted.juncs] [-m Memory limit] [-o Output directory] [-n Number of input files] [-c Config file path] Reads_filename</p> <p><strong>Outputs:</strong> Same as tuqueSplice</p> <h2 id="tuqueindex">tuqueIndex</h2> <p>tuqueIndex will prepare a Bowtie index including spliced sequences suitable for use with tuqueMap</p> <p><strong>Command line:</strong> tuqueIndex Genome_sequence_filename Read_length Splice_junctions.juncs Index_name_stem<br /> <strong>Outputs:</strong> A set of Bowtie index files</p> <h2 id="tuquemap">tuqueMap</h2> <p>tuqueMap will map a set of RNA-Seq reads to a genome using known splice junctions</p> <p><strong>Command line:</strong> tuqueMap [Options] bowtie_index Output_directory Reads_filename<br /> Options:<br /> -e The maximum sum of Phred quality values at all mismatched read positions [70]<br /> -h The maximum number of hits allowed for one read [25]<br /> -m The maximum amount of RAM to use, in bytes [10000000000]<br /> -n The maximum number of mismatches allowed in the first 28 bases of the read [3]<br /> -p The maximum number of processes to use [1].<br /> -c Path to configuration file [tuque/tuque.cfg]<br /> -a Path to .bam file containing Already-mapped reads [None]<br /> -u Keep uncompressed intermediate files</p> <p><strong>Outputs:</strong><br /> Read mappings in tuque_hits.bam<br /> Coverage depths in tuque.coverage.wig.gz<br /> bowtie.log contains read mapping statistics.</p> <h2 id="tuquecount">tuqueCount</h2> <p>tuqueCount will count the reads mapping inside annotated sequence features in a set of BAM files.</p> <p><strong>Command line:</strong> tuqueCount -g Annotation file [-o Output filename] [-c Config file path] Mapped reads filenames<br /> Options:<br /> -c Path to configuration file [tuque/tuque.cfg]<br /> -g The name of a GFF3 file containing the gene features to be counted. Required.<br /> -o Path to a file where output should be written [counts.txt].</p> <p><strong>Output:</strong> The output file is plain text with tab-delimited columns containing two sections. The first section has read counts as its data values and the second section has FPKM values. Each section contains a header line followed by a line for each sequence feature. Each line contains the feature ID, then its length, and then the data value for each input BAM file.<br /> This file can be imported by most spreadsheet programs.</p></div>Ian ReidWed, 10 Apr 2013 17:00:04 -0000https://sourceforge.net245484a9142b68349a78f3ab62c70f9bcd459d2e