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: Run Transdecoder on de novo contigs.
Make a new fasta of the longest ORFs at the protein level.
Summarize these numbers at the NT and AA level.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Ann Loraine [ aloraine ] | Brandon Bendickson [ bbendick ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Also ran on FCS filtered contigs. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Transdecoder/FCS_filtered_contigs
| Assignee | Brandon Bendickson [ bbendick ] | Robert Reid [ robertreid ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Significantly less putative proteins between filtered/unfiltered runs.
File: hei_longhit.fna.transdecoder.pep
Number of sequences: 55047
File: heinz_filtered.fa.transdecoder.pep
Number of sequences: 32447
These results look great.
| 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 ] |
successfully ran transdecoder on our unfiltered contigs. Results are found in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/Transdecoder/unfiltered_contigs