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1 <tool id="deseq-hts" name="DESeq" version="1.6.0">
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2 <description>Determines differentially expressed transcripts from read alignments</description>
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3 <command>
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4 deseq-hts/src/deseq-hts.sh $anno_input_selected $deseq_out $deseq_out.extra_files_path/gene_map.mat
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5 #for $i in $replicate_groups
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6 #for $j in $i.replicates
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7 $j.bam_alignment:#slurp
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8 #end for
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9 #end for
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10 >> $Log_File </command>
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11 <inputs>
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12 <param format="gff3" name="anno_input_selected" type="data" label="Genome annotation in GFF3 file" help="A tab delimited format for storing sequence features and annotations"/>
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13 <repeat name="replicate_groups" title="Replicate group" min="2">
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14 <repeat name="replicates" title="Replicate">
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15 <param format="bam" name="bam_alignment" type="data" label="BAM alignment file" help="BAM alignment file. Can be generated from SAM files using the SAM Tools."/>
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16 </repeat>
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17 </repeat>
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18 </inputs>
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19
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20 <outputs>
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21 <data format="txt" name="deseq_out" label="DESeq result"/>
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22 <data format="txt" name="Log_File" label="DESeq log file"/>
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23 </outputs>
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24
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25 <tests>
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26 <test>
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27 command:
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28 ./deseq-hts.sh ../test_data/deseq_c_elegans_WS200-I-regions.gff3 ../test_data/deseq_c_elegans_WS200-I-regions_deseq.txt ../test_data/genes.mat ../test_data/deseq_c_elegans_WS200-I-regions-SRX001872.bam ../test_data/deseq_c_elegans_WS200-I-regions-SRX001875.bam
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29
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30 <param name="anno_input_selected" value="deseq_c_elegans_WS200-I-regions.gff3" ftype="gff3" />
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31 <param name="bam_alignments1" value="deseq_c_elegans_WS200-I-regions-SRX001872.bam" ftype="bam" />
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32 <param name="bam_alignments2" value="deseq_c_elegans_WS200-I-regions-SRX001875.bam" ftype="bam" />
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33 <output name="deseq_out" file="deseq_c_elegans_WS200-I-regions_deseq.txt" />
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34 </test>
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35 </tests>
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36
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37 <help>
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38
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39 .. class:: infomark
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40
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41 **What it does**
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42
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43 `DESeq` is a tool for differential expression testing of RNA-Seq data.
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44
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45
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46 **Inputs**
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47
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48 `DESeq` requires three input files to run:
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49
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50 1. Annotation file in GFF3, containing the necessary information about the transcripts that are to be quantified.
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51 2. The BAM alignment files grouped into replicate groups, each containing several replicates. BAM files store the read alignments in a compressed format. They can be generated using the `SAM-to-BAM` tool in the NGS: SAM Tools section. (The script will also work with only two groups containing only a single replicate each. However, this analysis has less statistical power and is therefor not recommended.)
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52
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53 **Output**
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54
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55 `DESeq` generates a text file containing the gene name and the p-value.
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56
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57 ------
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58
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59 **Licenses**
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60
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61 If **DESeq** is used to obtain results for scientific publications it
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62 should be cited as [1]_.
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63
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64 **References**
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65
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66 .. [1] Anders, S and Huber, W (2010): `Differential expression analysis for sequence count data`_.
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67
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68 .. _Differential expression analysis for sequence count data: http://dx.doi.org/10.1186/gb-2010-11-10-r106
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69
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70 ------
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71
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72 .. class:: infomark
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73
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74 **About formats**
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75
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76
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77 **GFF3 format** General Feature Format is a format for describing genes
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78 and other features associated with DNA, RNA and protein
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79 sequences. GFF3 lines have nine tab-separated fields:
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80
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81 1. seqid - The name of a chromosome or scaffold.
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82 2. source - The program that generated this feature.
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83 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
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84 4. start - The starting position of the feature in the sequence. The first base is numbered 1.
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85 5. stop - The ending position of the feature (inclusive).
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86 6. score - A score between 0 and 1000. If there is no score value, enter ".".
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87 7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
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88 8. phase - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
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89 9. attributes - All lines with the same group are linked together into a single item.
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90
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91 For more information see http://www.sequenceontology.org/gff3.shtml
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92
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93 **SAM/BAM format** The Sequence Alignment/Map (SAM) format is a
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94 tab-limited text format that stores large nucleotide sequence
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95 alignments. BAM is the binary version of a SAM file that allows for
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96 fast and intensive data processing. The format specification and the
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97 description of SAMtools can be found on
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98 http://samtools.sourceforge.net/.
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99
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100 ------
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101
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102 DESeq-hts Wrapper Version 0.3 (Feb 2012)
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103
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104 </help>
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105 </tool>
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