Heatmap of read coverages
Created: 2014-04-03 14:39:20
Galaxy workflow based on deepTools which creates a clustered heatmap of the read coverage. Two BAM files will be used as input and a heatmap will be the output.
For more information please see the deepTools wiki. This workflow is also available via the Galaxy Tool Shed.
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Workflow Components
Inputs (12)
Name |
Description |
file 1 of mapped reads, e.g. treated sample |
|
file 2 of mapped reads, e.g. control sample |
|
regions |
|
region |
runtime parameter for tool bamCompare |
advancedOpt |
runtime parameter for tool bamCompare |
fragmentLength |
runtime parameter for tool bamCompare |
output |
runtime parameter for tool heatmapper |
advancedOpt |
runtime parameter for tool heatmapper |
advancedOpt |
runtime parameter for tool heatmapper |
advancedOpt |
runtime parameter for tool heatmapper |
advancedOpt |
runtime parameter for tool heatmapper |
advancedOpt |
runtime parameter for tool heatmapper |
Steps (6)
Name |
Tool |
Description |
Input dataset |
None |
|
Input dataset |
None |
|
Input dataset |
None |
|
bamCompare |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_bamCompare/1.1.0 |
|
computeMatrix |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_computeMatrix/1.1.0 |
|
heatmapper |
toolshed.g2.bx.psu.edu/repos/bgruening/deeptools/deeptools_heatmapper/1.1.0 |
|
Outputs (9)
Name |
Type |
outFileName |
bigwig |
outFileName |
bgzip |
outFileNameData |
tabular |
outFileSortedRegions |
bed |
outFileNameMatrix |
tabular |
outFileName |
png |
outFileNameData |
tabular |
outFileSortedRegions |
bed |
outFileNameMatrix |
tabular |
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Version 1
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