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1 <tool id="ReadLengthDistributionMatrix" name="Create read length distribution matrix" version="1.0.0">
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2 <description>across a genomic interval</description>
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3 <command interpreter="sh">galaxyToolRunner.sh ngs.ReadLengthDistributionMatrix -i $input --chr $chr --start $start --stop $stop --min $min --max $max --bin $bin -o $output</command>
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4 <inputs>
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5 <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" />
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6 <param name="chr" type="text" label="Chromosome" />
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7 <param name="start" type="integer" value="1" label="Start base pair" />
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8 <param name="stop" type="integer" value="1000" label="Stop base pair" />
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9 <param name="min" type="integer" value="1" label="Minimum fragment length (bp)" />
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10 <param name="max" type="integer" value="200" label="Maximum fragment length (bp)" />
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11 <param name="bin" type="integer" value="1" label="Fragment length bin size (bp)" />
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12 </inputs>
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13 <outputs>
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14 <data format="tabular" name="output" />
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15 </outputs>
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16
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17 <help>
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18
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19 This tool will create a matrix (in matrix2png_ format) with the distribution of read lengths over each base pair. Reads are binned by genomic location and length to create a matrix where each column represents the distribution of read lengths over that base pair. The resulting matrix can be turned into heatmap using the Visualization -> Make heatmap with matrix2png tool.
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20
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21 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html
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22
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23 .. class:: warningmark
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24
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25 This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length.
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26
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27 -----
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28
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29 **Syntax**
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30
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31 - **Mapped reads** are the mapped paired-end reads used to make the histograms
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32 - **Chromosome** a locus in the genome
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33 - **Start base pair** a locus in the genome
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34 - **Stop base pair** a locus in the genome
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35 - **Minimum fragment length** is the lowest fragment length bin. Reads shorter than this will be ignored.
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36 - **Maximum fragment length** is the highest fragment length bin. Reads longer than this will be ignored.
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37 - **Fragment length bin size** is the bin size used when making the fragment length histograms
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38
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39 -----
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40
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41 **Example**
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42
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43 Make a matrix with the read length distribution across the region chrI:5001-6000, looking at reads 100-200bp in length in bins of 1bp:
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44
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45 - **Chromosome:** chrI
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46 - **Start:** 5001
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47 - **Stop:** 6000
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48 - **Minimum fragment length:** 100
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49 - **Maximum fragment length:** 200
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50 - **Fragment length bin size:** 1
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51
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52 The resulting matrix will be 1000x101, with each column representing a base pair and each row representing a read length. The column headers give the base pair and the row headers give the read length.
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53
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54 -----
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55
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56 **Citation**
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57
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58 This tool was inspired by the analysis and figures in
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59
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60 Floer M, Wang X, Prabhu V, Berrozpe G, Narayan S, Spagna D, Alvarez D, Kendall J, Krasnitz A, Stepansky A, Hicks J, Bryant GO and Ptashne M (2010) A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding. Cell 141: 407–418
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61
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62 </help>
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63 </tool>
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