Details
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Type:
Task
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:None
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Story Points:1
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Sprint:Spring 2019 Sprint 3, Summer 2019 Sprint 8, Summer 2019 Sprint 10, Summer 2019 Sprint 11, Summer 2019 Sprint 12, Fall 2019 Sprint 1, Fall 2019 Sprint 2, Fall 2019 Sprint 3
Description
Situation: Aim 4 of the IGB-CyVerse grant uses an example app to make a coverage graph from a BAM file using CyVerse HPC infrastructure.
Tasks:
Investigate the current apps/tools available through the Discovery Environment.
Determine if any current tools/apps would be sufficient.
If a tool/app is sufficient, implement it in the Discovery Environment.
Attachments
Issue Links
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- Closed
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Activity
I have implemented a bedtools genomecov app in the DE that will produce a coverage graph in bedgraph format. The app is currently not public, as it requires some additional testing (paired-end data) and updated documentation within the DE before being made public (once public no additional edits can be made). This tool may also be superseded by a deeptools bamcoverage app, however I am still waiting for DE staff to add the tool.
I have moved this to first level review. Currently only members of the CyVerse team will have access to this tool (as it cannot be made public yet).
To Test:
Upload the example BAM and index to your CyVerse DE.
If you are a CyVerse team member, the tool "IGB Bedtools Genome Coverage" should be shared with you.
Run the analysis using the DE UI or Postman (see the Terrain API documentation).
Load the same example BAM file in IGB, and generate a depth graph .
Load the bedgraph generated in CyVerse into IGB.
The graphs should be the same (human genome (HG38) on chromosome 3).