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Stampy-build-and-
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map
Community rating: ?????
Stampy is a package for the mapping of next gen sequencing reads onto a reference genome. Stampy excels in the mapping of reads containing sequence variation relative to the reference, especially indels.
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- To use Stampy-build-and-map, import your data in ___ formatfastq format.
- Resources:http://replacewww.withwell.URLox.for.tool.documentation.from.the.tool.source.orgac.uk/project-stampy
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> directory.Stampy |
Input File(s)
Use TerriblyIncomprehensible.txt and HorriblyWritten.txt from the test_1.fastq file from the directory above as test input with the genome sequence provided, NC_010473.fa.
Parameters Used in App
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- Default
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- parameters
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- Default parameters only, no further configuration needed.
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- Use these parameters within the DE app interface:
- parameter name - value/setting parameter name - value/settingonly, except set the output file name to stampyout.sam
Output File(s)
Expect a text SAM file named after the input files as output. For stampyout.sam as output in the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.
Tool Source for App
- http://replacewww.withwell.URLox.for.tool.orgac.uk/project-stampy