http://stab.st-andrews.ac.uk/wiki/index.php?action=history&feed=atom&title=Mapping.py 2026-05-07T17:16:47Z Revision history for this page on the wiki MediaWiki 1.30.0 http://stab.st-andrews.ac.uk/wiki/index.php?title=Mapping.py&diff=1141&oldid=prev 2017-02-23T11:48:10Z

<p></p> <table class="diff diff-contentalign-left" data-mw="interface"> <col class="diff-marker" /> <col class="diff-content" /> <col class="diff-marker" /> <col class="diff-content" /> <tr style="vertical-align: top;" lang="en"> <td colspan="2" style="background-color: white; color:black; text-align: center;">← Older revision</td> <td colspan="2" style="background-color: white; color:black; text-align: center;">Revision as of 11:48, 23 February 2017</td> </tr><tr><td colspan="2" class="diff-lineno" id="mw-diff-left-l1" >Line 1:</td> <td colspan="2" class="diff-lineno">Line 1:</td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>= Introduction =</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>= Introduction =</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>−</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #ffe49c; vertical-align: top; white-space: pre-wrap;"><div>Another part of Miguel <del class="diffchange diffchange-inline">Pnheiros </del>script_tools suite.</div></td><td class='diff-marker'>+</td><td style="color:black; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #a3d3ff; vertical-align: top; white-space: pre-wrap;"><div>Another part of Miguel <ins class="diffchange diffchange-inline">Pinheiro&#039;s </ins>script_tools suite<ins class="diffchange diffchange-inline">. This takes paired-end FASTQ reads and generates a cleaned-up bam file from them</ins>.</div></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"></td></tr> <tr><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>= Outline =</div></td><td class='diff-marker'>&#160;</td><td style="background-color: #f9f9f9; color: #333333; font-size: 88%; border-style: solid; border-width: 1px 1px 1px 4px; border-radius: 0.33em; border-color: #e6e6e6; vertical-align: top; white-space: pre-wrap;"><div>= Outline =</div></td></tr> <!-- diff cache key wiki-bwik:diff:version:1.11a:oldid:1140:newid:1141 --> </table>

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<p>Created page with &quot;= Introduction = Another part of Miguel Pnheiros script_tools suite. = Outline = Each pair of FASTQ files are mapped to the reference. Bowtie, bwa or smalt are available....&quot;</p> <p><b>New page</b></p><div>= Introduction =<br /> <br /> Another part of Miguel Pnheiros script_tools suite.<br /> <br /> = Outline =<br /> <br /> Each pair of FASTQ files are mapped to the reference. Bowtie, bwa or smalt are available.<br /> run_soft.run_bwa_map(self.sz_sample_name, sz_out_directory, self.sz_index_file, self.sz_file_1, self.sz_file_2, self.sz_single_file, self.n_read_length)<br /> <br /> The output sam is converted to bam<br /> sz_cmd = &quot;%s view -bS %s%s.sam &gt; %s%s_.bam&quot; % (Constants.SOFTWARE_SAMTOOLS, sz_working_directory, sz_sample_name, sz_working_directory, sz_sample_name)<br /> <br /> This bam is then sorted<br /> sz_cmd = &quot;%s sort %s%s_.bam %s%s__&quot; % (Constants.SOFTWARE_SAMTOOLS, sz_working_directory, sz_sample_name, sz_working_directory, sz_sample_name)<br /> <br /> The MarkDuplicates tool from picard-tools is used to clean out redundant alignments<br /> sz_cmd = &quot;java -jar %s/MarkDuplicates.jar INPUT=%s%s__.bam OUTPUT=%s%s.bam M=%s%s_%s.txt&quot; % (Constants.SOFTWARE_PICARD_TOOLS_DIRECTORY, sz_working_directory, sz_sample_name,<br /> <br /> This duplicate-marked bam file is then indexed with normal (i.e. not tabix, tabular index):<br /> sz_cmd = &quot;%s index %s%s.bam&quot; % (Constants.SOFTWARE_SAMTOOLS, sz_working_directory, sz_sample_name)<br /> <br /> We delete the unecessary bam and sams:<br /> <br /> sz_cmd = &quot;rm %s%s_.bam %s%s__.bam %s%s.sam&quot; % (sz_working_directory, sz_sample_name, sz_working_directory, sz_sample_name, sz_working_directory, sz_sample_name)<br /> <br /> The end bam files are in fact the duplicate-marked files, so we are ready, but we also generate a coverage report from them:<br /> sz_cmd = &quot;%s/genomeCoverageBed -ibam %s%s.bam -bga &gt; %s%s.cov&quot; % (Constants.SOFTWARE_BED_TOOLS, sz_working_directory, sz_sample_name, sz_working_directory, sz_sample_name)</div>

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