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:2
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Epic Link:
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Sprint:Spring 3
Description
GOAL:
To write a script on the cluster based on previous scripts to BLAST
our de novo contigs against the 4 main contaminants found via the FCS filter tool.
The 4 contaminants are in:
/projects/tomato_genome/db/contaminants/
- sclerotinia_minor
- Sclerotinia_sclerotiorum
- Pseudocercospora_ulei
- Cladosporium_colombiae
These were pulled from NCBI as full genomes.
Need to makeblastDB for each contaminant.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Storing BLAST information on this sheet: https://docs.google.com/spreadsheets/d/1HeMRLHCuAZsEoXIq4sxLkK8qyuVMRkBzTQBsngx2IdE/edit?usp=sharing
Note: This is related to ticket IGBF-4093, the tomato mold story.
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| 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 ] |
-rerun at 1e-25
-get unique query IDs
-get number of hits
-make chart with this info