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:3
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Epic Link:
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Sprint:Summer 1
Description
GOAL:
To use the newly annotated Trinity files as a REFERENCE to align reads to and determine gene expression for Kelsey's dataset.
There are 4 newly generated Trinity sets of contigs (TMNH). See IGBF-3741.
Want to run NEXTFLOW. One for each variety.
Location of Trinity COntigs:
/projects/tomato_genome/fnb/dataprocessing/trinity/NEXTFLOW/postblat
(there should be 4 fasta files here, if not yet, soon.....)
The reads that will be used are here:
/projects/tomato_genome/rnaseq/renamed_Ravi_Combined
Instead of running ALL reads, we be separating by variety.
So only using the reads fr heinz with the Heinz trinity contig file......
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-2993 [ 21429 ] |
| Assignee | Ann Loraine [ aloraine ] | Robert Reid [ robertreid ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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 ] |