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annotate slamdunk.xml @ 1:9dfecde9fa06 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
author iuc
date Sun, 20 Jan 2019 06:50:55 -0500
parents a4de8b7d6f10
children 4b677ea9314a
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9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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1 <tool id="slamdunk" name="Slamdunk" version="@TOOL_VERSION@+galaxy1">
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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2 <description>- streamlining SLAM-seq analysis with ultra-high sensitivity</description>
1
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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3 <macros>
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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4 <import>macros.xml</import>
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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5 </macros>
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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6 <expand macro="requirements" />
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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7 <version_command>slamdunk --version</version_command>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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8 <command detect_errors="exit_code"><![CDATA[
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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9 #if $reference_source.reference_source_selector == 'history':
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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10 ln -f -s '$reference_source.ref_file' reference.fa &&
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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11 #else:
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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12 ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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13 #end if
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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14 slamdunk all -r reference.fa -b '$Reference' -o ./out
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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15 -n $multimapper.multimappers
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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16 $multimapper.multimap
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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17 #if $multimapper.filterbed.bedtofilter:
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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18 -fb $multimapper.filterbed.bedtofilter
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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19 #end if
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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20 -5 $quantseq.trim5
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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21 -a $quantseq.maxpolyA
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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22 $advanced.endtoend
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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23 -mq $advanced.minMQ
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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24 -mi $advanced.minID
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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25 -nm=$advanced.maxNM
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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26 -mc $advanced.minCov
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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27 -mv $advanced.minVar
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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28 -mbq $advanced.minBaseQual
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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29 -rl $readLength
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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30 -c $covThresh
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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31 '$Reads'
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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32 ]]></command>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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33 <inputs>
1
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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34 <expand macro="reference_files" />
9dfecde9fa06 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit dbd131d3a162e9d70c305148d305680acb549e93
iuc
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35 <param name="Reads" type="data" format="fastqsanger,fastqsanger.gz" label="FASTQ files"/>
0
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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36 <section name="multimapper" title="Multimapper recovery"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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37 expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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38 <section name="filterbed"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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39 title="Use separate 3' UTR bed to filter multimappers." expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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40 <param name="bedtofilter" type="data" format="bed" optional="true"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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41 label="Bed to filter" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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42 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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43 <param name="multimappers" type="integer" min="1" value="1"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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44 label="Maximum number of alignments to report per read"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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45 help="The maximum number of alignments is used to track multimapping read alignments. The more are allowed, the more sensitive the multimapper filtering will be, but also the longer the runtime will be. 100 was used in previous publications." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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46 <param name="multimap" type="boolean" truevalue="--multimap" falsevalue=""
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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47 label="Use reference bed file to resolve multimappers."
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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48 help="Enable multimapper recovery, requires -n to be set to a value > 1 to have impact." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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49 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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50 <section name="quantseq" title="Quantseq" expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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51 <param name="trim5" type="integer" min="0" value="12"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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52 label="Number of bp to remove from the 5' end of all reads"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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53 help="For Lexogen's Quantseq kit and previous SLAM-seq papers a clipping of 12 bp from the 5' end is recommended." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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54 <param name="maxpolyA" type="integer" min="0" value="4"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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55 label="Maximum number of As at the 3' end of a read"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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56 help="The maximum number of allowed As at the 3' end of a read. All A-stretches that exceed this threshold are clipped because they are likely part of the poly-A tail." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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57 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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58 <section name="advanced" title="Advanced settings." expanded="false">
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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59 <param name="endtoend" type="boolean" truevalue="--endtoend" falsevalue=""
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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60 label="Enable end-to-end alignments for mapping."
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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61 help="Enable end-to-end alignments for mapping in slamdunk with --endtoend" />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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62 <param name="minMQ" type="integer" min="0" value="2"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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63 label="Minimum mapping quality"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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64 help="Minimum mapping quality to consider alignments (default: 2)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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65 <param name="minID" type="float" min="0" value="0.95"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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66 label="Minimum alignment identity"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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67 help="Minimum alignment-identity to consider alignments (default: 0.95)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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68 <param name="maxNM" type="integer" value="-1"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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69 label="Maximum number of mismatches"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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70 help="Maximum number of mismatches to consider alignments. Negative numbers deactivate filter (default: -1)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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71 <param name="minCov" type="integer" min="0" value="10"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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72 label="Minimum coverage to call variant"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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73 help="Minimum coverage to call variant (default: 10)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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74 <param name="minVar" type="float" min="0" value="0.8"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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75 label="Minimum variant fraction to call variant"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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76 help="Minimum variant fraction to call variant (default: 0.8)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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77 <param name="minBaseQual" type="integer" min="0" value="27"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
iuc
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78 label="Minimum base quality"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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79 help="Minimum base quality for T>C conversions (default: 27)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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80 </section>
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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81 <param name="covThresh" type="integer" min="1" value="1"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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82 label="T>C conversion threshold"
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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83 help="Number of T>C conversions required to count a read as a T>C read (default: 1)." />
a4de8b7d6f10 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/slamdunk commit 1edb9bd1936e05d6a9ade3cde93b970fa89acb90
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84 <param name="readLength" type="integer" min="50" value="50"
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85 label="Read length"
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86 help="Maximum read length (before trimming)." />
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87 </inputs>
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88 <outputs>
1
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89 <data name="outputBam" format="bam" from_work_dir="./out/filter/*.bam" label="${tool.name} on ${on_string}: BAM"/>
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90 <data name="outputTsv" format="tabular" from_work_dir="./out/count/*_tcount.tsv" label="${tool.name} on ${on_string}: Count TSV"/>
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91 <data name="outputVcf" format="vcf" from_work_dir="./out/snp/*vcf" label="${tool.name} on ${on_string}: VCF"/>
0
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92 </outputs>
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93 <tests>
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94 <test>
1
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95 <!--Ensure default outputs work -->
0
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96 <param name="reference_source_selector" value="history" />
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97 <param name="ref_file" value="ref.fa" />
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98 <param name="Reference" value="actb.bed" />
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99 <param name="Reads" value="reads.fq" />
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100 <param name="readLength" value="100" />
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101 <section name="quantseq">
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102 <param name="trim5" value="0" />
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103 </section>
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104 <section name="advanced">
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105 <param name="minBaseQual" value="27" />
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106 </section>
1
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107 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
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108 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
0
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109 lines_diff="2" />
1
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110 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
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111 </test>
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112 <test>
1
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113 <!--Ensure built-in fasta works -->
0
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114 <param name="reference_source_selector" value="cached" />
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115 <param name="Reference" value="actb.bed" />
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116 <param name="Reads" ftype="fastqsanger" dbkey="hg38" value="reads.fq" />
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117 <param name="readLength" value="100" />
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118 <section name="quantseq">
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119 <param name="trim5" value="0" />
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120 </section>
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121 <section name="advanced">
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122 <param name="minBaseQual" value="27" />
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123 </section>
1
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124 <output name="outputBam" ftype="bam" file="reads1.bam" compare="sim_size"/>
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125 <output name="outputTsv" ftype="tabular" file="reads_slamdunk_mapped_filtered_tcount.tsv"
0
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126 lines_diff="2" />
1
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127 <output name="outputVcf" ftype="vcf" file="reads1_snp.vcf" compare="sim_size"/>
0
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128 </test>
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129 </tests>
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130 <help><![CDATA[
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131 SLAM-seq
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132 ========
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133
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134 SLAM-seq is a novel sequencing protocol that directly uncovers 4-thiouridine incorporation events in RNA by high-throughput sequencing. When combined with metabolic labeling protocols, SLAM-seq allows to study the intracellular RNA dynamics, from transcription, RNA processing to RNA stability.
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135
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136 Original publication: `Herzog et al., Nature Methods, 2017; doi:10.1038/nmeth.4435 <https://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4435.html>`_
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137
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138 Slamdunk
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139 ========
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140
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141 To analyze a given SLAM-seq dataset with *slamdunk* without recovering multimappers, you only need to provide the following files and keep everything else to the default parameters.
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142
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143 =============== ==========================================================================================================================================================
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144 Parameter Description
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145 =============== ==========================================================================================================================================================
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146 **Genome** The reference fasta file (Genome assembly).
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147 **Reference** BED-file containing coordinates for 3' UTRs.
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148 **Reads** Sample FASTQ(gz) files.
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149 **Read length** Maximum length of reads (usually 50, 100, 150).
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150 =============== ==========================================================================================================================================================
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151
1
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152 This will run the entire *slamdunk* analysis (`slamdunk all`) with the most relevant output files being:
0
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153
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154 * Tab-separated *tcount* file (Count TSV) containing the SLAM-seq statistics per UTR
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155 * BAM-file with the final filtered mapped reads
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156 * VCF file of variants called on the final filtered alignments
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157
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158 These files can be input to the **Alleyoop** tool for visualization and further processing. See the `Slamdunk documentation`_ for more information.
0
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159
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160 ------------------------------------------------------
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161
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162 Multimapper recovery
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163 --------------------
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164
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165 To utilize multimapper recovery, modify the following parameters. You must either choose a separate 3' UTR file or activate filtering
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166 on the supplied reference file. Will only yield different results than a unique-mapping run by specifying a number > 1 as maximum number of multimapper aligments to consider.
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167
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168 =================================================== =========================================================
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169 Parameter Description
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170 =================================================== =========================================================
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171 **Maximum number of alignments to report per read** The maximum number of multimapper alignments to consider.
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172 **Use separate 3' UTR bed to filter multimappers.** 3' UTR bed file to filter.
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173 **Use reference bed file to resolve multimappers.** Use reference as 3' UTR bed file to filter.
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174 =================================================== =========================================================
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175
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176 ------------------------------------------------------
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177
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178 T>C conversions
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179 ---------------
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180
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181 Depending on the use case, more stringent or more lenient measures of T>C conversion and T>C reads are required such as 2 T>C by `Muhar et al., Science, 2018; http://doi.org/10.1126/science.aao2793 <http://science.sciencemag.org/content/early/2018/04/04/science.aao2793>`_
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182
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183 This can be controlled by the following parameter:
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184
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185 ============================ ================================================================================
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186 Parameter Description
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187 ============================ ================================================================================
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188 **T>C conversion threshold** Minimum number of T>C conversions to consider a read as T>C read.
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189 ============================ ================================================================================
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190
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191 .. _`Slamdunk documentation`: http://t-neumann.github.io/slamdunk/docs.html
0
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192
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193 ]]></help>
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194 <citations>
1
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195 <expand macro="citations" />
0
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196 </citations>
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197 </tool>