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 10, Summer 1
Description
GOAL: Devise a strategy to annotate the Trinity results generated in IGBF-3647.
We have MANY contigs (170K or more per variety).
Step 1 would be to identify how many contigs align to a corresponding soly gene (via our blat results).
Step 2: How many trinity contigs fail to have a match?
Step 3: How many contigs are promiscuous and have many gene matches?
Step 4: How many Soly Ids have only 1 Trinity Contig match? (best hit recprical)
From this we will decide if these associations are suitable to be used as annotations.
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Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Robert Reid [ robertreid ] | Brandon Benkick [ bbendick ] |
| Sprint | Spring 10 [ 194 ] | Spring 10, Summer 1 [ 194, 195 ] |
| Rank | Ranked higher |
| Description |
GOAL: Devise a strategy to annotate the Trinity results generated in We have MANY contigs (170K or more per variety). Step 1 would be to identify how many contigs align to a corresponding soly gene (via our blat results). Step 2: How many trinity contigs fail to have a match? Step 3: How many contigs are promiscuous and have many gene matches? Step 4: How many Soly Ids have only 1 Trinity Contig match? (best hit recprical) From this we will decide if these associations are suitable to be used as annotations. |
GOAL: Devise a strategy to annotate the Trinity results generated in We have MANY contigs (170K or more per variety). Step 1 would be to identify how many contigs align to a corresponding soly gene (via our blat results). Step 2: How many trinity contigs fail to have a match? Step 3: How many contigs are promiscuous and have many gene matches? Step 4: How many Soly Ids have only 1 Trinity Contig match? (best hit recprical) From this we will decide if these associations are suitable to be used as annotations. |
| Comment |
[ I found out that Trinity v2.13 has a bug that prevents the creation of the output fasta files. I rewrote the script to use Trinity v2.14.0, but it is in the queue for Draco. Trying a test run on Orion with Trinity v2.14.0, will run the others using Orion if this one completes successfully. Scripts are located in /projects/tomato_genome/fnb/dataprocessing/brandon_work/nag/temp_trinity/trinity-nag.slurm
Patch notes for trinity updates: https://github.com/trinityrnaseq/trinityrnaseq/releases ] |
| 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 ] |