Mercurial > repos > timpalpant > java_genomics_toolkit
annotate galaxy-conf/ReadLengthDistributionMatrix.xml @ 25:b43c420a6135 draft default tip
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
| author | timpalpant |
|---|---|
| date | Sat, 09 Feb 2019 14:02:24 -0500 |
| parents | eb53be9a09f4 |
| children |
| rev | line source |
|---|---|
| 13 | 1 <tool id="ReadLengthDistributionMatrix" name="Create read length distribution matrix" version="1.0.0"> |
| 2 <description>across a genomic interval</description> | |
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b43c420a6135
Incorporate fix: https://github.com/timpalpant/java-genomics-toolkit/commit/9a6c61b7c6b8d85a1cd3f595eed657a537b85dc9
timpalpant
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13
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3 <command interpreter="bash">galaxyToolRunner.sh ngs.ReadLengthDistributionMatrix -i $input --chr $chr --start $start --stop $stop --min $min --max $max --bin $bin -o $output</command> |
| 13 | 4 <inputs> |
| 5 <param format="sam,bam,bed,bedgraph" name="input" type="data" label="Mapped reads" /> | |
| 6 <param name="chr" type="text" label="Chromosome" /> | |
| 7 <param name="start" type="integer" value="1" label="Start base pair" /> | |
| 8 <param name="stop" type="integer" value="1000" label="Stop base pair" /> | |
| 9 <param name="min" type="integer" value="1" label="Minimum fragment length (bp)" /> | |
| 10 <param name="max" type="integer" value="200" label="Maximum fragment length (bp)" /> | |
| 11 <param name="bin" type="integer" value="1" label="Fragment length bin size (bp)" /> | |
| 12 </inputs> | |
| 13 <outputs> | |
| 14 <data format="tabular" name="output" /> | |
| 15 </outputs> | |
| 16 | |
| 17 <help> | |
| 18 | |
| 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. | |
| 20 | |
| 21 .. _matrix2png: http://bioinformatics.ubc.ca/matrix2png/dataformat.html | |
| 22 | |
| 23 .. class:: warningmark | |
| 24 | |
| 25 This tool requires paired-end SAM, BAM, Bed, or BedGraph formatted data. Using single-end data will result in a constant read length. | |
| 26 | |
| 27 ----- | |
| 28 | |
| 29 **Syntax** | |
| 30 | |
| 31 - **Mapped reads** are the mapped paired-end reads used to make the histograms | |
| 32 - **Chromosome** a locus in the genome | |
| 33 - **Start base pair** a locus in the genome | |
| 34 - **Stop base pair** a locus in the genome | |
| 35 - **Minimum fragment length** is the lowest fragment length bin. Reads shorter than this will be ignored. | |
| 36 - **Maximum fragment length** is the highest fragment length bin. Reads longer than this will be ignored. | |
| 37 - **Fragment length bin size** is the bin size used when making the fragment length histograms | |
| 38 | |
| 39 ----- | |
| 40 | |
| 41 **Example** | |
| 42 | |
| 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: | |
| 44 | |
| 45 - **Chromosome:** chrI | |
| 46 - **Start:** 5001 | |
| 47 - **Stop:** 6000 | |
| 48 - **Minimum fragment length:** 100 | |
| 49 - **Maximum fragment length:** 200 | |
| 50 - **Fragment length bin size:** 1 | |
| 51 | |
| 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. | |
| 53 | |
| 54 ----- | |
| 55 | |
| 56 **Citation** | |
| 57 | |
| 58 This tool was inspired by the analysis and figures in | |
| 59 | |
| 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 | |
| 61 | |
| 62 </help> | |
| 63 </tool> |