{"id":580,"date":"2013-05-02T08:26:34","date_gmt":"2013-05-02T08:26:34","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=580"},"modified":"2014-06-09T11:17:26","modified_gmt":"2014-06-09T11:17:26","slug":"bowtie","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/bowtie\/","title":{"rendered":"Bowtie"},"content":{"rendered":"<h2>Overview<\/h2>\n<p>Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes.<\/p>\n<p>Version 0.12.9 &#038; 1.0.0 binaries are available on the CSF.<\/p>\n<h2>Restrictions on use<\/h2>\n<p>All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: <code>$BOWTIE_HOME\/$BOWTIE_VER\/COPYING<\/code><\/p>\n<p>For citation information see the <a href=\"http:\/\/bowtie-bio.sourceforge.net\/index.shtml\">Bowtie website<\/a>.<\/p>\n<h2>Set up procedure<\/h2>\n<p>To use the software you will need to load the modulefile:<\/p>\n<pre class>module load apps\/binapps\/bowtie\/1.0.0<\/pre>\n<pre class>module load apps\/binapps\/bowtie\/0.12.9<\/pre>\n<p>Indexes &#8211; No pre-built indexes have been installed. Users should download and build their own indexes and set the variable BOWTIE_INDEXES on the command line or in .bashrc . For example, in your scratch area:<\/p>\n<pre class=\"in1\">export BOWTIE_INDEXES=$HOME\/scratch\/my_indexes<\/pre>\n<h2>Running the application<\/h2>\n<p>Please do not run bowtie commands on the login node. qrsh is recommended for some commands. Computationally intense work should be done via the batch system.<\/p>\n<h3>Examples<\/h3>\n<ul>\n<li>Build the <code>AF293<\/code> reference into the build format <code>contig1.build<\/code> using the 1 hour compute node via <code>qrsh<\/code>:\n<pre>qrsh -V -l inter -l short -cwd bowtie-build AF293_REF.fasta contig1.build<\/pre>\n<\/li>\n<li>Run bowtie to builds a file of reads that don&#8217;t map to contig1 (AF293) using 8 cores via the batch system on the 1 hour node by writing a batch submission script:\n<pre>     \r\n#$ -V\r\n#$ -cwd\r\n#$ -pe smp.pe 8\r\n#$ -l short\r\n\r\nbowtie -S -q -p $NSLOTS contig1.build C023MABXX_3_5_1.fastq 351.sam --un unmapped351.fastq\r\n<\/pre>\n<\/li>\n<li>and submitting it thus:\n<pre>     \r\nqsub scriptname\r\n<\/pre>\n<\/li>\n<li>remove <code>-l short<\/code> if your job requires more than 1 hour. Perhaps replace with <code>-l twoday<\/code>.<\/li>\n<\/ul>\n<h2>Further info<\/h2>\n<ul>\n<li><a href=\"http:\/\/bowtie-bio.sourceforge.net\/manual.shtml\">Bowtie Manual<\/a><\/li>\n<li>Related applications available on the CSF: <\/li>\n<ul>\n<li><a href=\"\/csf-apps\/software\/applications\/bowtie2\">Bowtie2<\/a><\/li>\n<li><a href=\"\/csf-apps\/software\/applications\/cufflinks\">Cufflinks<\/a><\/li>\n<li><a href=\"\/csf-apps\/software\/applications\/samtools\">Samtools<\/a>\n<\/li>\n<li><a href=\"\/csf-apps\/software\/applications\/tophat\">Tophat<\/a><\/li>\n<\/ul>\n<\/ul>\n<\/ul>\n","protected":false},"excerpt":{"rendered":"<p>Overview Bowtie is an ultrafast, memory-efficient short read aligner geared toward quickly aligning large sets of short DNA sequences (reads) to large genomes. Version 0.12.9 &#038; 1.0.0 binaries are available on the CSF. Restrictions on use All users may access and use Bowtie. The software is open source. Users should consult the following file for further information: $BOWTIE_HOME\/$BOWTIE_VER\/COPYING For citation information see the Bowtie website. Set up procedure To use the software you will need.. <a href=\"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/bowtie\/\">Read more &raquo;<\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"parent":31,"menu_order":0,"comment_status":"open","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-580","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/580","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/comments?post=580"}],"version-history":[{"count":8,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/580\/revisions"}],"predecessor-version":[{"id":1514,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/580\/revisions\/1514"}],"up":[{"embeddable":true,"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/pages\/31"}],"wp:attachment":[{"href":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/wp-json\/wp\/v2\/media?parent=580"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}