MediaWiki API result
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{
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"fromtitle": "Main Page",
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"totitle": "Mapping reads with Mosaik",
"*": "<tr><td colspan=\"2\" class=\"diff-lineno\" id=\"mw-diff-left-l1\">Line 1:</td>\n<td colspan=\"2\" class=\"diff-lineno\">Line 1:</td></tr>\n<tr><td class=\"diff-marker\" data-marker=\"\u2212\"></td><td class=\"diff-deletedline diff-side-deleted\"><div><del class=\"diffchange diffchange-inline\">'''MediaWiki has been successfully installed</del>.<del class=\"diffchange diffchange-inline\">'''</del></div></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">Within the Pig ERC project we have several mapping strategies. This article describes the mapping procedure using Mosaik for paired-end mapping to the reference assembly</ins>.</div></td></tr>\n<tr><td class=\"diff-marker\"></td><td class=\"diff-context diff-side-deleted\"><br></td><td class=\"diff-marker\"></td><td class=\"diff-context diff-side-added\"><br></td></tr>\n<tr><td class=\"diff-marker\" data-marker=\"\u2212\"></td><td class=\"diff-deletedline diff-side-deleted\"><div><del class=\"diffchange diffchange-inline\">Consult </del>the <del class=\"diffchange diffchange-inline\">[http://meta</del>.<del class=\"diffchange diffchange-inline\">wikimedia</del>.<del class=\"diffchange diffchange-inline\">org/wiki/Help:Contents User's Guide] for information on using the wiki software</del>.</div></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">== Prerequisites ==</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== input reads ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">The mapping procedure requires paired end reads in fastq format. For </ins>the <ins class=\"diffchange diffchange-inline\">current procedure quality-trimmed reads are used</ins>. <ins class=\"diffchange diffchange-inline\">Forward and reverse reads should be in two separate files, and should be in the same order</ins>. <ins class=\"diffchange diffchange-inline\">Input files are assumed to have Sanger-style quality scaling</ins>.</div></td></tr>\n<tr><td class=\"diff-marker\"></td><td class=\"diff-context diff-side-deleted\"><br></td><td class=\"diff-marker\"></td><td class=\"diff-context diff-side-added\"><br></td></tr>\n<tr><td class=\"diff-marker\" data-marker=\"\u2212\"></td><td class=\"diff-deletedline diff-side-deleted\"><div>== <del class=\"diffchange diffchange-inline\">Getting started </del>==</div></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">Here the input fastq files are named 'reads_1_QT.fq.gz', for forward reads, and 'reads_2_QT.fq.gz' for reverse reads.</ins></div></td></tr>\n<tr><td class=\"diff-marker\" data-marker=\"\u2212\"></td><td class=\"diff-deletedline diff-side-deleted\"><div><del class=\"diffchange diffchange-inline\">* [http</del>://<del class=\"diffchange diffchange-inline\">www</del>.<del class=\"diffchange diffchange-inline\">mediawiki</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Manual</del>:<del class=\"diffchange diffchange-inline\">Configuration_settings Configuration settings list]</del></div></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td class=\"diff-marker\" data-marker=\"\u2212\"></td><td class=\"diff-deletedline diff-side-deleted\"><div><del class=\"diffchange diffchange-inline\">* [http</del>://<del class=\"diffchange diffchange-inline\">www</del>.<del class=\"diffchange diffchange-inline\">mediawiki</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">wiki</del>/<del class=\"diffchange diffchange-inline\">Manual:FAQ MediaWiki FAQ]</del></div></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>==<ins class=\"diffchange diffchange-inline\">= reference assembly files for MOSAIK =</ins>==</div></td></tr>\n<tr><td class=\"diff-marker\" data-marker=\"\u2212\"></td><td class=\"diff-deletedline diff-side-deleted\"><div><del class=\"diffchange diffchange-inline\">* [https:</del>//<del class=\"diffchange diffchange-inline\">lists</del>.<del class=\"diffchange diffchange-inline\">wikimedia</del>.<del class=\"diffchange diffchange-inline\">org</del>/<del class=\"diffchange diffchange-inline\">mailman</del>/<del class=\"diffchange diffchange-inline\">listinfo</del>/<del class=\"diffchange diffchange-inline\">mediawiki</del>-<del class=\"diffchange diffchange-inline\">announce MediaWiki release mailing list]</del></div></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">The procedure described here requires a number of MOSAIK specific input files: a '.dat' file of the reference assembly, and a so called 'jump' database. These can be found in</ins>:</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>/<ins class=\"diffchange diffchange-inline\">shared/Sus/Sscrofa_build10_2/</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">== Mapping procedure ==</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== creating MOSAIK file for the reads ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">The first step is creating '.dat' file of the sequence reads. </ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">MosaikBuild -q reads_1_QT.fq.gz -q2 reads_2_QT.fq.gz -out reads_QT.dat -st sanger</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== Align reads with MOSAIK ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">MosaikAligner -in reads_QT</ins>.<ins class=\"diffchange diffchange-inline\">dat -out aligned_reads</ins>.<ins class=\"diffchange diffchange-inline\">dat -ia /shared/Sus/Sscrofa_build10_2/Mosaiklibs</ins>/<ins class=\"diffchange diffchange-inline\">Ssc10_2_wUn.dat -hs 15 -mmp 0.07 -m all -mhp 10 -p 24 -act 20 -j </ins>/<ins class=\"diffchange diffchange-inline\">shared/Sus/Sscrofa_build10_2/Mosaiklibs/Ssc10_2_wUn.jump15</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">==== Sort the alignment file ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">MosaikSort -in aligned_reads.dat -out aligned_reads-sorted.dat</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">==== convert to BAM ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">MosaikText -in aligned_reads-sorted.dat -bam aligned_reads-sorted.bam</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">== Finalizing preparation of BAM files with SAMtools ==</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== prepare a new header file ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">samtools view -H aligned_reads-sorted.bam | sed 's/SM:unknown/SM:pigname/' | sed 's/PL</ins>:<ins class=\"diffchange diffchange-inline\">sanger/PL:ILLUMINA/' >newheader.txt</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">samtools view -H another_aligned_reads-sorted.bam | sed 's/SM:unknown/SM:pigname/' | sed 's/PL</ins>:<ins class=\"diffchange diffchange-inline\">sanger</ins>/<ins class=\"diffchange diffchange-inline\">PL:ILLUMINA</ins>/<ins class=\"diffchange diffchange-inline\">' | grep @RG >>newheader</ins>.<ins class=\"diffchange diffchange-inline\">txt</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== merge BAM files (if applicable) ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">samtools merge merged.bam aligned_reads-sorted.bam another_aligned_reads-sorted</ins>.<ins class=\"diffchange diffchange-inline\">bam</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== reheader merged BAM file ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">samtools reheader newheader.txt merged.bam >pigname_rh.bam</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">== Variant calling with Samtools ==</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== calling raw variants ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">samtools view -u pigname_rh.bam | samtools pileup -vcf /shared/Sus/Sscrofa_build10_2</ins>/<ins class=\"diffchange diffchange-inline\">FASTA</ins>/<ins class=\"diffchange diffchange-inline\">Ssc10_2_wUn</ins>.<ins class=\"diffchange diffchange-inline\">fa - >vars-raw_pigname</ins>.<ins class=\"diffchange diffchange-inline\">txt</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== filtering variants ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">samtools.pl varFilter -D25 vars-raw_pigname.txt | awk '($3==\"*\"&&$6>=50)||($3!=\"*\"&&$6>=20)' >vars-flt_pigname-final.txt</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><</ins>/<ins class=\"diffchange diffchange-inline\">pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">== Additional notes ==</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== submitting using grid-engine ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">Submitting jobs using the grid-engine (qsub) requires a few additional options. The following lines can be added to the script to be submitted:</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">#!/bin/bash</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">#$ -cwd</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">#$ -S /bin</ins>/<ins class=\"diffchange diffchange-inline\">sh</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">#$ </ins>-<ins class=\"diffchange diffchange-inline\">v MOSAIK_TMP=/srv/nfs02/yourhomedir/</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div>\u00a0</div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">=== Tidying up ===</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">Please clean up the intermediate files as soon as they are not needed any more.</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"><pre></ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">rm *.dat</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\">rm reads.bam</ins></div></td></tr>\n<tr><td colspan=\"2\" class=\"diff-side-deleted\"></td><td class=\"diff-marker\" data-marker=\"+\"></td><td class=\"diff-addedline diff-side-added\"><div><ins class=\"diffchange diffchange-inline\"></pre></ins></div></td></tr>\n"
}
}