Heatmap of read coverages

Created: 2014-04-03 14:39:20

Download Workflow

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.

Preview

Not available

Import

Not currently available.

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