[IGBF-4045] NEXTFLOW using TSA contigs as reference, using raw reads as input - JIRA UNCC

Details

Type: Task
Status: Closed (View Workflow)
Priority: Major
Resolution: Done
Affects Version/s: None
Fix Version/s: None
Labels:
None

Story Points:
3
Epic Link:
Support NSF pollen grant
Sprint:
Winter 1

Description

GOAL: Another NEXTFLOW run using the TSA contigs as the reference.
We use the reads of Kelsies just like the original expt.

1. get NEXTFLOW to run
2. Summarize the alignments

Once this is done, we make a new ticket and start DESEQ2 * 4 varieties and compare time points and overall general patterns if there are any.

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Robert Reid created issue - 08/Jan/25 11:17 AM

Robert Reid made changes - 08/Jan/25 11:17 AM

Field	Original Value	New Value
Epic Link		IGBF-2993 [ 21429 ]

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Brandon Bendickson added a comment - 08/Jan/25 3:15 PM

Heinz run using TSA contigs as reference has completed without error. Results and files are located in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW/Hei_1

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Brandon Bendickson added a comment - 08/Jan/25 3:15 PM Heinz run using TSA contigs as reference has completed without error. Results and files are located in: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW/Hei_1

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Robert Reid added a comment - 08/Jan/25 4:00 PM

Great!!
Does this needs repeating for the other 3 varieties?

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Robert Reid added a comment - 08/Jan/25 4:00 PM Great!! Does this needs repeating for the other 3 varieties? R

Brandon Bendickson made changes - 08/Jan/25 4:02 PM

Status

To-Do [ 10305 ]

In Progress [ 3 ]

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Brandon Bendickson added a comment - 08/Jan/25 4:02 PM

Yes, will continue and run for rest of the varieties

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Brandon Bendickson added a comment - 08/Jan/25 4:02 PM Yes, will continue and run for rest of the varieties

Brandon Bendickson made changes - 10/Jan/25 9:25 AM

Status

In Progress [ 3 ]

Needs 1st Level Review [ 10005 ]

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Brandon Bendickson added a comment - 10/Jan/25 9:25 AM

Nextflow completed for all 4 varieties without error. Results of the 4 nextflow runs are found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW

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Brandon Bendickson added a comment - 10/Jan/25 9:25 AM Nextflow completed for all 4 varieties without error. Results of the 4 nextflow runs are found here: /projects/tomato_genome/fnb/dataprocessing/brandon_work/FCS-FILTER-NEXTFLOW

Brandon Bendickson made changes - 10/Jan/25 10:05 AM

Assignee

Brandon Bendickson [ bbendick ]

Robert Reid [ robertreid ]

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Robert Reid added a comment - 13/Jan/25 11:07 AM

I looked through and I see all of the bam files and salmon count tables.

We are good to move on to ticket #~~IGBF-4052~~, deseq on the read counts!!

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Robert Reid added a comment - 13/Jan/25 11:07 AM I looked through and I see all of the bam files and salmon count tables. We are good to move on to ticket # IGBF-4052 , deseq on the read counts!!