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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Epic Link:
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Sprint:Winter 1
Description
GOAL:
To get familiar with Interproscan so that we can annotate the remaining genes that lack an SL5 or NR DB annotation.
Need to get the tool ready for using. It has been a few years since it has been used and the ENV has changed. Hopefully the tool still works as is.
We need to identify what sequences we wish to run through.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Successfully ran on 2 of the tomato groups on the cluster. Going to relaunch and get outputs for the other two that did not complete.
Results will be found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/InterProScan/newest_version/interproscan-5.72-103.0/outputdir
Interpro analysis for all 4 varieties has completed and results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/InterProScan/newest_version/interproscan-5.72-103.0/outputdir
Assigning to Dr. Reid to take a look at results.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
This as first glance looks like the data we'd expect.
Next phase!!
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
1st steps:
Make a sequences file 1000 and run it through the web based version.