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IGVtools count (USER MANUAL UNDER DEVELOPMENT)
IGVtools count
Community rating: ?????
The "count" command computes average feature density over a specified window size across the genome. Common usages include computing coverage for alignment files and counting hits in Chip-seq experiments.
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- To use IGVtools count, import your data in ___ SAM, BAM, or BED format.
Resources
more info: http://replacewww.with.URL.for.tool.documentation.from.the.tool.source.org
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| Info |
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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. htseq_count |
Input File(s)
Use TerriblyIncomprehensible.txt and HorriblyWritten.txt testfile.sam from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
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- Default 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/setting
Output File(s)
Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.
Tool Source for App
- http://replace.with.URL.for.tool.orgwww.broadinstitute.org/igv/book/export/html/72